2OEZ | pdb_00002oez

Protein of Unknown Function (DUF1342) from Vibrio parahaemolyticus

PDB DOI: https://doi.org/10.2210/pdb2OEZ/pdb

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

Deposited: 2007-01-02 Released: 2007-01-30
Deposition Author(s): Kim, Y., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.267 (Depositor), 0.264 (DCC)
R-Value Work:
0.210 (Depositor), 0.207 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2OEZ

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the Protein of Unknown Function VP2528 from Vibrio parahaemolyticus

Kim, Y., Volkart, L., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 57.9 kDa
Atom Count: 4,932
Modeled Residue Count: 484
Deposited Residue Count: 494
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0289 protein VP2528	A, B	247	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 5 Gene Names: VP2528
UniProt
Find proteins for Q87LT3 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87LT3 Go to UniProtKB: Q87LT3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87LT3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.267 (Depositor), 0.264 (DCC)
R-Value Work: 0.210 (Depositor), 0.207 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.759	α = 90
b = 77.567	β = 90
c = 146.167	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-01-30

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-01-30
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: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: 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.