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BMRB: 25281

2N2M

NMR STRUCTURE OF YERSINIA PESTIS AIL (ATTACHMENT INVASION LOCUS) IN DECYLPHOSPHOCHOLINE MICELLES

Authors

Ding, Y., Yao, Y., Fujimoto, L.M., Marassi, F.M.

Assembly

YERSINIA PESTIS AIL (ATTACHMENT INVASION LOCUS)

Entity

1. YERSINIA PESTIS AIL (ATTACHMENT INVASION LOCUS) (polymer, Thiol state: not present), 156 monomers, 17471.21 Da Detail

EGESSISIGY AQSRVKEDGY KLDKNPRGFN LKYRYEFNND WGVIGSFAQT RRGFEESVDG FKLIDGDFKY YSVTAGPVFR INEYVSLYGL LGAGHGKAKF SSIFGQSESR SKTSLAYGAG LQFNPHPNFV IDASYEYSKL DDVKVGTWML GAGYRF

Formula weight

17471.21 Da

Source organism

Yersinia pestis KIM10+

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 37.4 %, Completeness (bb): 66.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	37.4 % (684 of 1828)	23.3 % (221 of 948)	44.1 % (315 of 715)	89.7 % (148 of 165)
Backbone	66.1 % (613 of 928)	52.1 % (171 of 328)	66.1 % (296 of 448)	96.1 % (146 of 152)
Sidechain	19.4 % (201 of 1036)	8.1 % (50 of 620)	37.0 % (149 of 403)	15.4 % (2 of 13)
Aromatic	4.0 % (10 of 248)	4.0 % (5 of 124)	4.1 % (5 of 122)	0.0 % (0 of 2)
Methyl	16.2 % (21 of 130)	12.3 % (8 of 65)	20.0 % (13 of 65)

1. ATTACHMENT INVASION LOCUS PROTEIN

EGESSISIGY AQSRVKEDGY KLDKNPRGFN LKYRYEFNND WGVIGSFAQT RRGFEESVDG FKLIDGDFKY YSVTAGPVFR INEYVSLYGL LGAGHGKAKF SSIFGQSESR SKTSLAYGAG LQFNPHPNFV IDASYEYSKL DDVKVGTWML GAGYRF

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	ATTACHMENT INVASION LOCUS PROTEIN	[U-13C; U-15N]	0.5 mM
2	potassium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	5 mM
4	decylphosphocholine	natural abundance	170 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2N2M, Strand ID: A Detail

Release date

2015-07-19

Citation

Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation
Marassi, F.M., Ding, Y., Schwieters, C.D., Tian, Y., Yao, Y.
J. Biomol. NMR (2015), 63, 59-65, PubMed 26143069 , DOI 10.1007/s10858-015-9963-2 , Abstract

Related entities 1. YERSINIA PESTIS AIL (ATTACHMENT INVASION LOCUS), : 1 : 4 : 1 : 14 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 20 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25281_2n2m.nef
Input source #2: Coordindates	2n2m.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
EGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESVDGFKLIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESVDGFKLIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKF

-------110-------120-------130-------140-------150------
SSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	156	0	0	100.0

Content subtype: combined_25281_2n2m.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	572		96.2 (chain: A, length: 156)
1	Distance restraints	CNS/XPLOR_distance_constraints_14	Warning	30 (1)	noe	21.2 (chain: A, length: 156)
2	Distance restraints	CNS/XPLOR_distance_constraints_8	Warning	19 (1)	noe	10.9 (chain: A, length: 156)
3	Distance restraints	CNS/XPLOR_distance_constraints_12	Warning	22 (1)	noe	14.7 (chain: A, length: 156)
4	Distance restraints	CNS/XPLOR_distance_constraints_18	Warning	15 (1)	noe	12.8 (chain: A, length: 156)
5	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	14 (1)	noe	10.9 (chain: A, length: 156)
6	Distance restraints	CNS/XPLOR_distance_constraints_10	Warning	15 (1)	noe	11.5 (chain: A, length: 156)
7	Distance restraints	CNS/XPLOR_distance_constraints_16	Warning	19 (1)	noe	11.5 (chain: A, length: 156)
8	Distance restraints	CNS/XPLOR_distance_constraints_20	Warning	14 (1)	noe	10.9 (chain: A, length: 156)
9	Distance restraints	CNS/XPLOR_distance_constraints_24	Warning	9 (1)	hbond	6.4 (chain: A, length: 156)
10	Distance restraints	CNS/XPLOR_distance_constraints_32	Warning	8 (1)	hbond	5.1 (chain: A, length: 156)
11	Distance restraints	CNS/XPLOR_distance_constraints_26	Warning	10 (1)	hbond	6.4 (chain: A, length: 156)
12	Distance restraints	CNS/XPLOR_distance_constraints_36	Warning	9 (1)	hbond	7.7 (chain: A, length: 156)
13	Distance restraints	CNS/XPLOR_distance_constraints_22	Warning	8 (1)	hbond	6.4 (chain: A, length: 156)
14	Distance restraints	CNS/XPLOR_distance_constraints_34	Warning	10 (1)	hbond	6.4 (chain: A, length: 156)
15	Distance restraints	CNS/XPLOR_distance_constraints_30	Warning	11 (1)	hbond	9.0 (chain: A, length: 156)
16	Distance restraints	CNS/XPLOR_distance_constraints_28	Warning	12 (1)	hbond	8.3 (chain: A, length: 156)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	240 (240)	.	92.3 (chain: A, length: 156)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	12 (12)	.	9.6 (chain: A, length: 156)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 96.2%
- Total number of assignments
  - ¹H chemical shifts: 146
  - ¹³C chemical shifts: 280
  - ¹⁵N chemical shifts: 146
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	948	146	15.4
¹³C chemical shifts	715	280	39.2
¹⁵N chemical shifts	173	146	84.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	328	146	44.5
¹³C chemical shifts	312	150	48.1
¹⁵N chemical shifts	152	146	96.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	620	0	0.0
¹³C chemical shifts	403	130	32.3
¹⁵N chemical shifts	21	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	0	0.0
¹³C chemical shifts	66	9	13.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	0	0.0
¹³C chemical shifts	122	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_14
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 21.2%
- Total number of restraints: 30
- Weight of restraints: 1.0 (30)
- Potential type of restraints: square-well-parabolic (30)
- Range of distance target values: 2.7, 3.8 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_8
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 10.9%
  - Total number of restraints: 19
  - Weight of restraints: 1.0 (19)
  - Potential type of restraints: square-well-parabolic (19)
  - Range of distance target values: 2.7, 3.8 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_12
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 14.7%
    - Total number of restraints: 22
    - Weight of restraints: 1.0 (22)
    - Potential type of restraints: square-well-parabolic (22)
    - Range of distance target values: 2.7, 3.8 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_18
      - Status: Warning
      - Experiment type: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 12.8%
      - Total number of restraints: 15
        Medium range restraints, 1 < | i - j | < 5 : 1
        Backbone-backbone: 1
        Long range restraints, | i - j | >= 5 : 14
      - Weight of restraints: 1.0 (15)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (1)
        Backbone-backbone: 1.0 (1)
        Long range restraints, | i - j | >= 5 : 1.0 (14)
      - Potential type of restraints: square-well-parabolic (15)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (1)
        Backbone-backbone: square-well-parabolic (1)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (14)
      - Range of distance target values: 2.7, 3.8 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
      - Saveframe: CNS/XPLOR_distance_constraints_6
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 10.9%
        Total number of restraints: 14
        Long range restraints, | i - j | >= 5 : 14
        Weight of restraints: 1.0 (14)
        Long range restraints, | i - j | >= 5 : 1.0 (14)
        Potential type of restraints: square-well-parabolic (14)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (14)
        Range of distance target values: 2.7, 3.8 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_10
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 11.5%
        Total number of restraints: 15
        Long range restraints, | i - j | >= 5 : 15
        Weight of restraints: 1.0 (15)
        Long range restraints, | i - j | >= 5 : 1.0 (15)
        Potential type of restraints: square-well-parabolic (15)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (15)
        Range of distance target values: 2.7, 3.8 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_16
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 11.5%
        Total number of restraints: 19
        Medium range restraints, 1 < | i - j | < 5 : 4
        Backbone-backbone: 1
        Backbone-side chain: 3
        Long range restraints, | i - j | >= 5 : 15
        Weight of restraints: 1.0 (19)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (4)
        Backbone-backbone: 1.0 (1)
        Backbone-side chain: 1.0 (3)
        Long range restraints, | i - j | >= 5 : 1.0 (15)
        Potential type of restraints: square-well-parabolic (19)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (4)
        Backbone-backbone: square-well-parabolic (1)
        Backbone-side chain: square-well-parabolic (3)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (15)
        Range of distance target values: 2.7, 3.8 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_20
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 10.9%
        Total number of restraints: 14
        Long range restraints, | i - j | >= 5 : 14
        Weight of restraints: 1.0 (14)
        Long range restraints, | i - j | >= 5 : 1.0 (14)
        Potential type of restraints: square-well-parabolic (14)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (14)
        Range of distance target values: 2.7, 3.8 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_24
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 6.4%
        Total number of restraints: 9
        Total hydrogen bond restraints: 9
        Weight of restraints: 1.0 (9)
        Total hydrogen bond restraints: 1.0 (9)
        Potential type of restraints: square-well-parabolic (9)
        Total hydrogen bond restraints: square-well-parabolic (9)
        Range of distance target values: 2.1, 2.1 (Å)
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_32
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 5.1%
        Total number of restraints: 8
        Total hydrogen bond restraints: 8
        Weight of restraints: 1.0 (8)
        Total hydrogen bond restraints: 1.0 (8)
        Potential type of restraints: square-well-parabolic (8)
        Total hydrogen bond restraints: square-well-parabolic (8)
        Range of distance target values: 2.1, 2.1 (Å)
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_26
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 6.4%
        Total number of restraints: 10
        Total hydrogen bond restraints: 10
        Weight of restraints: 1.0 (10)
        Total hydrogen bond restraints: 1.0 (10)
        Potential type of restraints: square-well-parabolic (10)
        Total hydrogen bond restraints: square-well-parabolic (10)
        Range of distance target values: 2.1, 2.1 (Å)
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_36
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 7.7%
        Total number of restraints: 9
        Total hydrogen bond restraints: 9
        Weight of restraints: 1.0 (9)
        Total hydrogen bond restraints: 1.0 (9)
        Potential type of restraints: square-well-parabolic (9)
        Total hydrogen bond restraints: square-well-parabolic (9)
        Range of distance target values: 2.1, 2.1 (Å)
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_22
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 6.4%
        Total number of restraints: 8
        Total hydrogen bond restraints: 8
        Weight of restraints: 1.0 (8)
        Total hydrogen bond restraints: 1.0 (8)
        Potential type of restraints: square-well-parabolic (8)
        Total hydrogen bond restraints: square-well-parabolic (8)
        Range of distance target values: 2.1, 2.1 (Å)
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_34
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 6.4%
        Total number of restraints: 10
        Total hydrogen bond restraints: 10
        Weight of restraints: 1.0 (10)
        Total hydrogen bond restraints: 1.0 (10)
        Potential type of restraints: square-well-parabolic (10)
        Total hydrogen bond restraints: square-well-parabolic (10)
        Range of distance target values: 2.1, 2.1 (Å)
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_30
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 9.0%
        Total number of restraints: 11
        Total hydrogen bond restraints: 11
        Weight of restraints: 1.0 (11)
        Total hydrogen bond restraints: 1.0 (11)
        Potential type of restraints: square-well-parabolic (11)
        Total hydrogen bond restraints: square-well-parabolic (11)
        Range of distance target values: 2.1, 2.1 (Å)
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: CNS/XPLOR_distance_constraints_28
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 8.3%
        Total number of restraints: 12
        Total hydrogen bond restraints: 12
        O...H-x: 2
        Long range: 10
        O...H-x: 10
        Weight of restraints: 1.0 (12)
        Total hydrogen bond restraints: 1.0 (12)
        O...H-x: 1.0 (2)
        Long range: 1.0 (10)
        O...H-x: 1.0 (10)
        Potential type of restraints: square-well-parabolic (12)
        Total hydrogen bond restraints: square-well-parabolic (12)
        O...H-x: square-well-parabolic (2)
        Long range: square-well-parabolic (10)
        O...H-x: square-well-parabolic (10)
        Range of distance target values: 2.1, 2.1 (Å)
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 92.3%
- Total number of restraints: 240
- Total number of restraints per polymer type: 240
- Weight of restraints: 1.0 (240)
- Potential type of restraints: square-well-parabolic (240)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_4
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 9.6%
  - Total number of restraints: 12
  - Total number of restraints per polymer type: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: square-well-parabolic (12)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue

Keywords membrane protein

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BMRB: 25281

Sample

Chemical shift reference

Chemical shift reference

Related entities 1. YERSINIA PESTIS AIL (ATTACHMENT INVASION LOCUS), : 1 : 4 : 1 : 14 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

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Instrument

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Instrument

Sample

NMR combined restraints 20 contents Detail