3BK5 | pdb_00003bk5

Crystal structure of putative outer membrane lipoprotein-sorting protein domain from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3BK5/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-12-05 Released: 2008-02-05 
• Deposition Author(s): Wu, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

The crystal structure of putative outer membrane lipoprotein-sorting protein domain from Vibrio parahaemolyticus.

Wu, R., Abdullah, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 27.72 kDa 
• Atom Count: 2,141 
• Modeled Residue Count: 235 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative outer membrane lipoprotein-sorting protein	A	237	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VP1287
UniProt
Find proteins for Q87Q63 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87Q63  Go to UniProtKB:  Q87Q63

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.157	α = 90
b = 128.874	β = 90
c = 41.968	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: 2008-02-05 
Deposition Author(s): Wu, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary