3OF4 | pdb_00003of4

Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb3OF4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Idiomarina loihiensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-08-13 Released: 2010-08-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.194 (Depositor), 0.199 (DCC)
R-Value Work:
0.157 (Depositor), 0.168 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 75.13 kDa
Atom Count: 5,749
Modeled Residue Count: 624
Deposited Residue Count: 627
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitroreductase	A, B, C	209	Idiomarina loihiensis	Mutation(s): 0 Gene Names: nfnB, IL2077
UniProt
Find proteins for Q5R179 (Idiomarina loihiensis (strain ATCC BAA-735 / DSM 15497 / L2-TR)) Explore Q5R179 Go to UniProtKB: Q5R179
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5R179
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain AA [auth C]	AA [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain AA [auth C] Interactions & Density Focus chain AA [auth C]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain D [auth A] MOL2 format, chain R [auth B] MOL2 format, chain D [auth A] mmCIF format, chain R [auth B] mmCIF format, chain D [auth A]	D [auth A], R [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain D [auth A] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain R [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] F [auth A] BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], S [auth B], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain P [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain P [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain P [auth A]	IA [auth C] J [auth A] JA [auth C] K [auth A] KA [auth C] IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], P [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
UNL Query on UNL Download:Ideal Coordinates CCD File	E [auth A], Q [auth B]	Unknown ligand QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain Q [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.194 (Depositor), 0.199 (DCC)
R-Value Work: 0.157 (Depositor), 0.168 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.702	α = 90
b = 74.051	β = 112.49
c = 64.565	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-25
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: 2024-11-06
Changes: Data collection, 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.