2P3Y | pdb_00002p3y

Crystal structure of VPA0735 from Vibrio parahaemolyticus. NorthEast Structural Genomics target VpR109

PDB DOI: https://doi.org/10.2210/pdb2P3Y/pdb

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

Deposited: 2007-03-10 Released: 2007-03-27
Deposition Author(s): Seetharaman, J., Neely, H., Forouhar, F., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.234 (Depositor)
R-Value Work:
0.204 (Depositor)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of VPA0735 from Vibrio parahaemolyticus.

Seetharaman, J., Neely, H., Forouhar, F., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 114.01 kDa
Atom Count: 8,142
Modeled Residue Count: 922
Deposited Residue Count: 982
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein VPA0735	A, B	491	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 16 Gene Names: VPA0735
UniProt
Find proteins for Q87I71 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87I71 Go to UniProtKB: Q87I71
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87I71
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: 1.80 Å
R-Value Free: 0.234 (Depositor)
R-Value Work: 0.204 (Depositor)
R-Value Observed: 0.204 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.764	α = 84.81
b = 64.253	β = 89.14
c = 78.524	γ = 76.47

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-03-27

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-03-27
Type: Initial release
Version 1.1: 2008-01-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2018-01-24
Changes: Database references, Structure summary
Version 1.4: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary