3PXV

Crystal structure of a Nitroreductase with bound FMN (Dhaf_2018) from Desulfitobacterium hafniense DCB-2 at 2.30 A resolution

PDB DOI: https://doi.org/10.2210/pdb3PXV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Desulfitobacterium hafniense DCB-2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-10 Released: 2010-12-29
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.235
R-Value Work: 0.174
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a Nitroreductase with bound FMN (Dhaf_2018) from Desulfitobacterium hafniense DCB-2 at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 86.39 kDa
Atom Count: 6,235
Modelled Residue Count: 754
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitroreductase	A, B, C, D	189	Desulfitobacterium hafniense DCB-2	Mutation(s): 0 Gene Names: Dhaf_2018, YP_002458491.1
UniProt
Find proteins for B8FRE0 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FRE0 Go to UniProtKB: B8FRE0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8FRE0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.235
R-Value Work: 0.174
R-Value Observed: 0.177
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33PXV

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.261	α = 90
b = 81.577	β = 90
c = 161.754	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-12-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.