3NLC | pdb_00003nlc

Crystal structure of the VP0956 protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR147

PDB DOI: https://doi.org/10.2210/pdb3NLC/pdb

Classification: Structural Genomics, Unknown function
Organism(s): Vibrio parahaemolyticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-06-21 Released: 2010-08-18
Deposition Author(s): Vorobiev, S., Neely, H., Seetharaman, J., Wang, D., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.271 (Depositor), 0.279 (DCC)
R-Value Work:
0.215 (Depositor)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the VP0956 protein from Vibrio parahaemolyticus.

Vorobiev, S., Neely, H., Seetharaman, J., Wang, D., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.

To be published.

Macromolecule Content

Total Structure Weight: 61.66 kDa
Atom Count: 4,225
Modeled Residue Count: 534
Deposited Residue Count: 549
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein VP0956	A	549	Vibrio parahaemolyticus	Mutation(s): 1 Gene Names: VP0956
UniProt
Find proteins for Q87R42 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87R42 Go to UniProtKB: Q87R42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87R42
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 2.15 Å
R-Value Free: 0.271 (Depositor), 0.279 (DCC)
R-Value Work: 0.215 (Depositor)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.079	α = 90
b = 78.166	β = 90
c = 101.875	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXDE	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-08-18

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-08-18
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