2OYZ | pdb_00002oyz

Crystal structure of unknown function protein VPA0057 from Vibrio parahaemolyticus (targeted domain 2-94)

PDB DOI: https://doi.org/10.2210/pdb2OYZ/pdb

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

Deposited: 2007-02-23 Released: 2007-03-20
Deposition Author(s): Chang, C., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.237 (Depositor), 0.265 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2OYZ

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of unknown function protein VPA0057 from Vibrio parahaemolyticus

Chang, C., Volkart, L., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 10.25 kDa
Atom Count: 917
Modeled Residue Count: 94
Deposited Residue Count: 94
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0345 protein VPA0057	A	94	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 2 Gene Names: VPA0057 EC: 2.4.2.1 (UniProt), 2.4.2.2 (UniProt)
UniProt
Find proteins for Q87K41 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87K41 Go to UniProtKB: Q87K41
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87K41
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.237 (Depositor), 0.265 (DCC)
R-Value Work: 0.203 (Depositor)
R-Value Observed: 0.205 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.302	α = 90
b = 37.302	β = 90
c = 135.555	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-03-20

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-03-20
Type: Initial release
Version 1.1: 2007-11-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.