4DN2 | pdb_00004dn2

CRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metallireducens GS-15

PDB DOI: https://doi.org/10.2210/pdb4DN2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Geobacter metallireducens GS-15
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-08 Released: 2012-02-22
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.194 (Depositor), 0.203 (DCC)
R-Value Work:
0.152 (Depositor), 0.161 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metallireducens GS-15

Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 47.36 kDa
Atom Count: 3,233
Modelled Residue Count: 381
Deposited Residue Count: 416
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	208	Geobacter metallireducens GS-15	Mutation(s): 0 Gene Names: ABB33053.1, Gmet_2835
UniProt
Find proteins for Q39RS1 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)) Explore Q39RS1 Go to UniProtKB: Q39RS1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q39RS1
Sequence Annotations Expand
Reference Sequence LOADING

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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 1.50 Å
R-Value Free: 0.194 (Depositor), 0.203 (DCC)
R-Value Work: 0.152 (Depositor), 0.161 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.884	α = 90
b = 64.161	β = 98.14
c = 61.384	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-22

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-02-22
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 4DN2 | pdb_00004dn2

CRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metallireducens GS-15

CRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metallireducens GS-15

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

4DN2 | pdb_00004dn2