3I8N | pdb_00003i8n

A domain of a conserved functionally known protein from Vibrio parahaemolyticus RIMD 2210633.

• PDB DOI: https://doi.org/10.2210/pdb3I8N/pdb

• Classification: structural genomics, unknown function
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-09 Released: 2009-09-01 
• Deposition Author(s): Tan, K., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.265 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

A domain of a conserved functionally known protein from Vibrio parahaemolyticus RIMD 2210633.

Tan, K., Tesar, C., Bearden, 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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.1 kDa 
• Atom Count: 2,120 
• Modeled Residue Count: 250 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein VP2912	A, B	130	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: Vibrio parahaemolyticus, VP2912
UniProt
Find proteins for Q87KR4 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87KR4  Go to UniProtKB:  Q87KR4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-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: 2.15 Å
• R-Value Free:  0.265 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.301	α = 90
b = 69.301	β = 90
c = 255.136	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Tan, K., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary