2OD0 | pdb_00002od0

The crystal structure of gene product VP1028 from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb2OD0/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-12-21 Released: 2007-01-23 
• Deposition Author(s): Zhang, R., Zhou, M., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.245 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

The crystal structure of gene product VP1028 from Vibrio parahaemolyticus

Zhang, R., Zhou, M., Moy, S., 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)

Macromolecule Content 

• Total Structure Weight: 25.21 kDa 
• Atom Count: 1,895 
• Modeled Residue Count: 205 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein VP1028	A, B	105	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 4  Gene Names: VP1028
UniProt
Find proteins for Q87QX1 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87QX1  Go to UniProtKB:  Q87QX1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.245 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.458	α = 90
b = 42.876	β = 90
c = 157.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Zhang, R., Zhou, M., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Structure summary