1ZOV | pdb_00001zov

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.191 (Depositor), 0.202 (DCC)
R-Value Work:
0.158 (Depositor), 0.169 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23342
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.191 (Depositor), 0.202 (DCC)
R-Value Work: 0.158 (Depositor), 0.169 (DCC)
R-Value Observed: 0.159 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-05-23

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2024-10-23
Changes: Structure summary