3C85

Crystal structure of TrkA domain of putative glutathione-regulated potassium-efflux KefB from Vibrio parahaemolyticus

PDB DOI: https://doi.org/10.2210/pdb3C85/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio parahaemolyticus RIMD 2210633
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-02-08 Released: 2008-03-04
Deposition Author(s): Wu, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of TrkA domain of putative glutathione-regulated potassium-efflux KefB from Vibrio parahaemolyticus.

Wu, R., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 82.54 kDa
Atom Count: 4,590
Modelled Residue Count: 552
Deposited Residue Count: 732
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutathione-regulated potassium-efflux system protein KefB	A, B, C, D	183	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0 Gene Names: VP0827
UniProt
Find proteins for Q87RG9 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87RG9 Go to UniProtKB: Q87RG9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87RG9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain G [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.733	α = 90
b = 66.382	β = 90
c = 145.357	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-03-04

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-03-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.