1NNI

Azobenzene Reductase from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb1NNI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-01-13 Released: 2003-07-29
Deposition Author(s): Cuff, M.E., Kim, Y., Maj, L., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.238
R-Value Work: 0.221
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Azobenzene Reductase from Bacillus subtilis

Cuff, M.E., Kim, Y., Maj, L., Collart, F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 19.66 kDa
Atom Count: 1,478
Modelled Residue Count: 171
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein yhda	A [auth 1]	174	Bacillus subtilis	Mutation(s): 0 Gene Names: yhda EC: 1.7.1.6
UniProt
Find proteins for O07529 (Bacillus subtilis (strain 168)) Explore O07529 Go to UniProtKB: O07529
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O07529
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 B [auth 1] MOL2 format, chain B [auth 1]	B [auth 1]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth 1] Interactions & Density Focus chain B [auth 1]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.238
R-Value Work: 0.221
R-Value Observed: 0.223
Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.72	α = 90
b = 112.72	β = 90
c = 90.011	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-07-29

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2003-07-29
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-11-16
Changes: Atomic model

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.