BMRBj - BMREntryMaster

Found 1 Document (0.802 seconds)

BMRB: 15504

2JW1

Structural characterization of the type III pilotin-secretin interaction in Shigella flexneri by NMR spectroscopy

Authors

Okon, M.S., Lario, P.I., Creagh, L., Jung, Y.M. T., Maurelli, A.T., Strynadka, N.C.J., McIntosh, L.P.

Assembly

MxiM - MxiD complex

Entity

1. MxiM(28-142) (polymer, Thiol state: all disulfide bound), 115 monomers, 12886.74 Da Detail

SSSNSEKEWH IVPVSKDYFS IPNDLLWSFN TTNKSINVYS KCISGKAVYS FNAGKFMGNF NVKEVDGCFM DAQKIAIDKL FSMLKDGVVL KGNKINDTIL IEKDGEVKLK LIRGI

2. MxiD(553-570) (polymer, Thiol state: not present), 19 monomers, 2130.306 Da Detail

SETTLLEDEK SLVSYLNYX

Total weight

15017.046 Da

Max. entity weight

12886.74 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS42:SG	1:CYS68:SG

Source organism

Shigella flexneri

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.0 %, Completeness: 88.2 %, Completeness (bb): 86.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.2 % (1404 of 1592)	93.5 % (772 of 826)	82.8 % (514 of 621)	81.4 % (118 of 145)
Backbone	86.5 % (687 of 794)	94.9 % (258 of 272)	82.4 % (322 of 391)	81.7 % (107 of 131)
Sidechain	88.9 % (821 of 923)	92.8 % (514 of 554)	83.4 % (296 of 355)	78.6 % (11 of 14)
Aromatic	88.4 % (122 of 138)	94.2 % (65 of 69)	82.1 % (55 of 67)	100.0 % (2 of 2)
Methyl	91.3 % (137 of 150)	98.7 % (74 of 75)	84.0 % (63 of 75)

1. MxiM(28-142)

SSSNSEKEWH IVPVSKDYFS IPNDLLWSFN TTNKSINVYS KCISGKAVYS FNAGKFMGNF NVKEVDGCFM DAQKIAIDKL FSMLKDGVVL KGNKINDTIL IEKDGEVKLK LIRGI

2. MxiD(553-570)

SETTLLEDEK SLVSYLNYX

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 (±0.5) K, pH 6.5 (±0.1), Details 20 mM HEPES and 0.5 mM of dodecylmaltoside were present in solution.

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2JW1, Strand ID: A, B Detail

Release date

2008-10-30

Citation

Structural characterization of the type-III pilot-secretin complex from Shigella flexneri
Okon, M., Moraea, T.F., Lario, P.I., Creagh, L., Haynes, C.A., Strynadka, N.C.J., McIntosh, L.P.
Structure (2008), 16, 1544-1554, PubMed 18940609 , DOI 10.1016/j.str.2008.08.006 , Abstract

Entries sharing articles BMRB: 3 entries Detail

  BMRB: 15497 released on 2008-10-30
    Title Backbone 1H, 13C, and 15N Chemical Shift Assignments for MxiD in complex with MxiM
  BMRB: 15503 released on 2008-10-30
    Title Backbone 1H, 13C, and 15N Chemical Shift Assignments for MxiM(28-142)
  BMRB: 7407 released on 2008-10-30
    Title Backbone 1H, 13C, and 15N Chemical Shift Assignments for MxiD in complex with MxiM

Related entities 1. MxiM(28-142), : 1 : 3 entities Detail

Related entities 2. MxiD(553-570), : 1 : 2 entities Detail

Interaction partners 1. MxiM(28-142), : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Interaction partners 2. MxiD(553-570), : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 (±0.5) K, pH 6.5 (±0.1), Details 20 mM HEPES and 0.5 mM of dodecylmaltoside were present in solution.

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

4 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

5 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

9 13C/15N_F1,F2-filtered_NOESY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

10 13C/15N_F1,F2-filtered_TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MxiM(28-142)	[U-95% 13C; U-95% 15N]	0.3 - 0.5 mM
2	MxiD(553-570)	natural abundance	0.5 - 0.7 mM
3	HEPES	natural abundance	20 mM
4	dodecylmaltosid	natural abundance	0.5 mM
5	H2O	natural abundance	95 %
6	D2O		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15504_2jw1.nef
Input source #2: Coordindates	2jw1.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:69:CYS:SG	A:95:CYS:SG	unknown	unknown	2.028

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:2:SER:N	2:1:ACE:C	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	552	ACE	ACETYL GROUP	Coordinates

Sequence alignments

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

--30-------40--------50--------60--------70--------80--------90-------100-------110-------120-------
SSSNSEKEWHIVPVSKDYFSIPNDLLWSFNTTNKSINVYSKCISGKAVYSFNAGKFMGNFNVKEVDGCFMDAQKIAIDKLFSMLKDGVVLKGNKINDTIL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SSSNSEKEWHIVPVSKDYFSIPNDLLWSFNTTNKSINVYSKCISGKAVYSFNAGKFMGNFNVKEVDGCFMDAQKIAIDKLFSMLKDGVVLKGNKINDTIL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

130-------140--
IEKDGEVKLKLIRGI
|||||||||||||||
IEKDGEVKLKLIRGI
-------110-----

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

------560-------570
XSETTLLEDEKSLVSYLNY
|||||||||||||||||||
XSETTLLEDEKSLVSYLNY
--------10---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0
B	B	19	0	0	100.0

Content subtype: combined_15504_2jw1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1401		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3897 (1)	noe	95.7 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 95.7%
- Total number of restraints: 3893
- Weight of restraints: 1.0 (3893)
- Potential type of restraints: square-well-parabolic (3893)
- Range of distance target values: 1.42, 6.68 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords Membrane proteins, NMR, Pilot protein, Protein structure, Proten-protein interaction, protein-protein interaction

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Found 1 Document (0.802 seconds)

BMRB: 15504

Sample

Entries sharing articles BMRB: 3 entries Detail

Related entities 1. MxiM(28-142), : 1 : 3 entities Detail

Related entities 2. MxiD(553-570), : 1 : 2 entities Detail

Interaction partners 1. MxiM(28-142), : 1 interactors Detail

Interaction partners 2. MxiD(553-570), : 1 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail