3BW4 | pdb_00003bw4

Crystal structures and site-directed mutagenesis study of nitroalkane oxidase from Streptomyces ansochromogenes

PDB DOI: https://doi.org/10.2210/pdb3BW4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces ansochromogenes
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-01-08 Released: 2009-01-13
Deposition Author(s): Li, Y.H., Gao, Z.Q., Hou, H.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.216 (Depositor), 0.190 (DCC)
R-Value Work:
0.185 (Depositor), 0.180 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures and site-directed mutagenesis study of nitroalkane oxidase from Streptomyces ansochromogenes

Li, Y.H., Gao, Z.Q., Hou, H.F., Dong, Y.H., Tan, H.R.

To be published.

Macromolecule Content

Total Structure Weight: 39.1 kDa
Atom Count: 2,705
Modeled Residue Count: 347
Deposited Residue Count: 369
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-nitropropane dioxygenase	A	369	Streptomyces ansochromogenes	Mutation(s): 1 Gene Names: 2-npdl EC: 1.7.3.1
UniProt
Find proteins for Q9FDD4 (Streptomyces ansochromogenes) Explore Q9FDD4 Go to UniProtKB: Q9FDD4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FDD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.216 (Depositor), 0.190 (DCC)
R-Value Work: 0.185 (Depositor), 0.180 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.319	α = 90
b = 113.319	β = 90
c = 115.334	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-01-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description

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.