2QIP | pdb_00002qip

Crystal structure of a protein of unknown function VPA0982 from Vibrio parahaemolyticus RIMD 2210633

• PDB DOI: https://doi.org/10.2210/pdb2QIP/pdb

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


• Deposited: 2007-07-05 Released: 2007-07-24 
• Deposition Author(s): Tan, K., Duggan, E., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

The crystal structure of a protein of unknown function, VPA0982 from Vibrio parahaemolyticus RIMD 2210633.

Tan, K., Duggan, E., 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.

Macromolecule Content 

• Total Structure Weight: 19.36 kDa 
• Atom Count: 1,527 
• Modeled Residue Count: 162 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein of unknown function VPA0982	A	165	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 2  Gene Names: VPA0982
UniProt
Find proteins for Q9AF14 (Vibrio parahaemolyticus) Explore Q9AF14  Go to UniProtKB:  Q9AF14

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.48 Å
• R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.207	α = 90
b = 75.034	β = 90
c = 80.418	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Tan, K., Duggan, E., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary