2R5S | pdb_00002r5s

The crystal structure of a domain of protein VP0806 (unknown function) from Vibrio parahaemolyticus RIMD 2210633

• PDB DOI: https://doi.org/10.2210/pdb2R5S/pdb

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


• Deposited: 2007-09-04 Released: 2007-09-18 
• Deposition Author(s): Tan, K., Wu, R., Abdullah, J., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

The crystal structure of a domain of protein VP0806 (unknown function) from Vibrio parahaemolyticus RIMD 2210633.

Tan, K., Wu, R., Abdullah, J., Freeman, L., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.64 kDa 
• Atom Count: 2,850 
• Modeled Residue Count: 342 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein VP0806	A, B	176	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VP0806
UniProt
Find proteins for Q87RI8 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87RI8  Go to UniProtKB:  Q87RI8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], G [auth B], H [auth B], I [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 2.14 Å
• R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.001	α = 90
b = 116.476	β = 88.75
c = 62.224	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-18 
Deposition Author(s): Tan, K., Wu, R., Abdullah, J., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary