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Found 1 Document (0.708 seconds)

BMRB: 30284

5VJ8

Backbone structure of the Yersinia pestis outer membrane protein Ail in phospholipid bilayer nanodisc

Authors

Dutta, S.K., Yong, Y., Marassi, F.M.

Assembly

Adhesion invasion locus

Entity

1. Adhesion 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

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 65.4 %, Completeness: 18.6 %, Completeness (bb): 33.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	18.6 % (340 of 1828)	13.8 % (131 of 948)	15.7 % (112 of 715)	58.8 % (97 of 165)
Backbone	33.1 % (307 of 928)	31.7 % (104 of 328)	24.1 % (108 of 448)	62.5 % (95 of 152)
Sidechain	3.7 % (38 of 1036)	4.5 % (28 of 620)	2.0 % (8 of 403)	15.4 % (2 of 13)
Aromatic	1.6 % (4 of 248)	1.6 % (2 of 124)	0.0 % (0 of 122)	100.0 % (2 of 2)
Methyl	1.5 % (2 of 130)	1.5 % (1 of 65)	1.5 % (1 of 65)

1. entity 1

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

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.66 mM [U-13C; U-15N; U-2H] Ail, 49.5 mM DMPC, 16.5 mM DMPG, 5 mM sodium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
1	Ail	[U-13C; U-15N; U-2H]	0.66 mM
2	DMPC	natural abundance	49.5 mM
3	DMPG	natural abundance	16.5 mM
4	sodium chloride	natural abundance	5 mM
5	sodium phosphate	natural abundance	25 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 5VJ8, Strand ID: A Detail

Release date

2017-05-07

Citation

Structural Insights into the Yersinia pestis Outer Membrane Protein Ail in Lipid Bilayers
Dutta, S.K., Yong, Y., Marassi, F.M.
J. Phys. Chem. B (2017), 121, 7561-7570, PubMed 28726410 , DOI 10.1021/acs.jpcb.7b03941 , Abstract

Related entities 1. Adhesion invasion locus, : 1 : 4 : 1 : 14 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30284_5vj8.nef
Input source #2: Coordindates	5vj8.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_30284_5vj8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	276		60.9 (chain: A, length: 156)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	37 (1)	noe	47.4 (chain: A, length: 156)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	67 (1)	hbond	46.2 (chain: A, length: 156)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	162 (162)	.	62.8 (chain: A, length: 156)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 60.9%
- Total number of assignments
  - ¹H chemical shifts: 91
  - ¹³C chemical shifts: 94
  - ¹⁵N chemical shifts: 91
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	91	9.6
¹³C chemical shifts	715	94	13.1
¹⁵N chemical shifts	173	91	52.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	328	89	27.1
¹³C chemical shifts	312	94	30.1
¹⁵N chemical shifts	152	89	58.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	620	2	0.3
¹³C chemical shifts	403	0	0.0
¹⁵N chemical shifts	21	2	9.5

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	2	1.6
¹³C chemical shifts	122	0	0.0
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 47.4%
- Total number of restraints: 37
- Weight of restraints: 1.0 (37)
- Potential type of restraints: square-well-parabolic (37)
- Range of distance target values: 3.0, 3.0 (Å)
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 46.2%
  - Total number of restraints: 67
  - Weight of restraints: 1.0 (67)
  - Potential type of restraints: square-well-parabolic (67)
  - 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: 62.8%
- Total number of restraints: 162
- Total number of restraints per polymer type: 162
- Weight of restraints: 1.0 (162)
- Potential type of restraints: square-well-parabolic (162)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Adhesion invasion locus, Nanodisc, beta-barrel, membrane protein

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Found 1 Document (0.708 seconds)

BMRB: 30284

Sample

Related entities 1. Adhesion invasion locus, : 1 : 4 : 1 : 14 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail