3C85 | pdb_00003c85

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.232 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	G [auth C]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	E [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary