1NNI | pdb_00001nni

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Azobenzene Reductase from Bacillus subtilis

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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 (PDB Primary Data), 1.7 (UniProt)
UniProt
Find proteins for O07529 (Bacillus subtilis (strain 168)) Explore O07529  Go to UniProtKB:  O07529

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth 1]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary