1ZOV

Crystal Structure of Monomeric Sarcosine Oxidase from Bacillus sp. NS-129

• PDB DOI: https://doi.org/10.2210/pdb1ZOV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus sp. NS-129
• Mutation(s): No 


• Deposited: 2005-05-14 Released: 2006-05-23 
• Deposition Author(s): Nagata, K., Sasaki, H., Ohtsuka, J., Hua, M., Okai, M., Kubota, K., Kamo, M., Ito, K., Ichikawa, T., Koyama, Y., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.191 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Literature

Crystal structure of monomeric sarcosine oxidase from Bacillus sp. NS-129 reveals multiple conformations at the active-site loop

Nagata, K., Sasaki, H., Hua, M., Okai, M., Kubota, K., Kamo, M., Ito, K., Ichikawa, T., Koyama, Y., Tanokura, M.

(2005) Proc Jpn Acad Ser B Phys Biol Sci 81: 220-224

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.22 kDa 
• Atom Count: 6,532 
• Modelled Residue Count: 761 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monomeric sarcosine oxidase	A, B	386	Bacillus sp. NS-129	Mutation(s): 0  EC: 1.5.3.1
UniProt
Find proteins for P23342 (Bacillus sp. (strain NS-129)) Explore P23342  Go to UniProtKB:  P23342

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.191 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.042	α = 90
b = 171.042	β = 90
c = 72.455	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-23 
Deposition Author(s): Nagata, K., Sasaki, H., Ohtsuka, J., Hua, M., Okai, M., Kubota, K., Kamo, M., Ito, K., Ichikawa, T., Koyama, Y., Tanokura, M.

Revision History  

• Version 1.0: 2006-05-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description