3C0D

Crystal structure of the putative nitrite reductase NADPH (small subunit) oxidoreductase protein Q87HB1. Northeast Structural Genomics Consortium target VpR162

PDB DOI: https://doi.org/10.2210/pdb3C0D/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio parahaemolyticus RIMD 2210633
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-19 Released: 2008-03-04
Deposition Author(s): Kuzin, A.P., Abashidze, M., Seetharaman, J., Vorobiev, S.M., Wang, D., Fang, Y., Owens, L., Ma, L.-C., Xiao, 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: 2.40 Å
R-Value Free:
0.274 (Depositor), 0.279 (DCC)
R-Value Work:
0.241 (Depositor), 0.251 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the putative nitrite reductase NADPH (small subunit) oxidoreductase protein Q87HB1.

Kuzin, A.P., Abashidze, M., Seetharaman, J., Vorobiev, S.M., Wang, D., Fang, Y., Owens, L., Ma, L.-C., Xiao, 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: 108.94 kDa
Atom Count: 6,722
Modelled Residue Count: 852
Deposited Residue Count: 952
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein	A, B, C, D, E A, B, C, D, E, F, G, H	119	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0 Gene Names: VPA1054
UniProt
Find proteins for Q87HB1 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87HB1 Go to UniProtKB: Q87HB1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q87HB1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.274 (Depositor), 0.279 (DCC)
R-Value Work: 0.241 (Depositor), 0.251 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.667	α = 90
b = 103.462	β = 91.37
c = 82.951	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-03-04

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-03-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references, Structure summary
Version 1.4: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary