3PXV | pdb_00003pxv

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 (Depositor), 0.239 (DCC)
R-Value Work:
0.174 (Depositor), 0.186 (DCC)
R-Value Observed:
0.177 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.4 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
Modeled Residue Count: 754
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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 (Depositor), 0.239 (DCC)
R-Value Work: 0.174 (Depositor), 0.186 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

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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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
Version 1.4: 2024-11-20
Changes: Data collection, Refinement description, 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.