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), 0.195 (DCC)
R-Value Work:
0.185 (Depositor), 0.191 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.195 (DCC)
R-Value Work: 0.185 (Depositor), 0.191 (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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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

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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.