3KOQ | pdb_00003koq

Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.58 A resolution

PDB DOI: https://doi.org/10.2210/pdb3KOQ/pdb

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

Deposited: 2009-11-13 Released: 2009-12-01
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.183 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Nitroreductase family protein (YP_001089872.1) from Clostridium difficile 630 at 1.58 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 92.34 kDa
Atom Count: 6,969
Modeled Residue Count: 689
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITROREDUCTASE FAMILY PROTEIN	A, B, C, D	191	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD3355
UniProt
Find proteins for Q180K0 (Clostridioides difficile (strain 630)) Explore Q180K0 Go to UniProtKB: Q180K0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q180K0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 J [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	E [auth A], J [auth B], P [auth C], T [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain T [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain I [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] M [auth B] F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B]

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: 1.58 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.178 (Depositor), 0.183 (DCC)
R-Value Observed: 0.180 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.369	α = 90
b = 87.924	β = 102.33
c = 87.501	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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-01

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Advisory, Data collection, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary