3GFA | pdb_00003gfa

Crystal structure of a putative nitroreductase in complex with fmn (cd3205) from clostridium difficile 630 at 1.35 A resolution

PDB DOI: https://doi.org/10.2210/pdb3GFA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-26 Released: 2009-03-17
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.157 (Depositor), 0.160 (DCC)
R-Value Work:
0.134 (Depositor), 0.140 (DCC)
R-Value Observed:
0.135 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative nitroreductase in complex with FMN (YP_001089721.1) from CLOSTRIDIUM DIFFICILE 630 at 1.35 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 47.04 kDa
Atom Count: 3,859
Modeled Residue Count: 393
Deposited Residue Count: 396
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 nitroreductase	A, B	198	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD3205, YP_001089721.1
UniProt
Find proteins for Q17ZU8 (Clostridioides difficile (strain 630)) Explore Q17ZU8 Go to UniProtKB: Q17ZU8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q17ZU8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

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: 1.35 Å
R-Value Free: 0.157 (Depositor), 0.160 (DCC)
R-Value Work: 0.134 (Depositor), 0.140 (DCC)
R-Value Observed: 0.135 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33GFA

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.336	α = 90
b = 109.891	β = 104.84
c = 60.635	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-16
Changes: Data collection, Structure summary

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Help and Resources

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Crystal structure of a putative nitroreductase in complex with fmn (cd3205) from clostridium difficile 630 at 1.35 A resolution

Crystal structure of putative nitroreductase in complex with FMN (YP_001089721.1) from CLOSTRIDIUM DIFFICILE 630 at 1.35 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations