3X22 | pdb_00003x22

Crystal structure of Escherichia coli nitroreductase NfsB mutant N71S/F123A/F124W

PDB DOI: https://doi.org/10.2210/pdb3X22/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-12-06 Released: 2015-11-18
Deposition Author(s): Bai, J., Yang, J., Zhou, Y., Yang, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.242 (Depositor)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structural basis of Escherichia coli nitroreductase NfsB triple mutants engineered for improved activity and regioselectivity toward the prodrug CB1954

Bai, J., Yang, J., Zhou, Y., Yang, Q.

(2015) Process Biochem 50: 1760-1766

DOI: https://doi.org/10.1016/j.procbio.2015.08.012

Macromolecule Content

Total Structure Weight: 53 kDa
Atom Count: 3,651
Modeled Residue Count: 434
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen-insensitive NAD(P)H nitroreductase	A, B	237	Escherichia coli K-12	Mutation(s): 3 Gene Names: nfnB, dprA, nfsB, nfsI, ntr EC: 1.5.1.34 (PDB Primary Data), 1 (UniProt)
UniProt
Find proteins for P38489 (Escherichia coli (strain K12)) Explore P38489 Go to UniProtKB: P38489
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38489
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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242 (Depositor)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.075	α = 90
b = 57.075	β = 90
c = 263.611	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-11-18
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.