2GF3 | pdb_00002gf3

Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb2GF3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus sp. (in: firmicutes)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-21 Released: 2007-02-06 
• Deposition Author(s): Chen, Z., Trickey, P., Jorns, M.S., Mathews, F.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.195 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.177 (DCC) 

Starting Model: experimental

Literature

Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 A resolution.

Chen, Z., Trickey, P., Jorns, M.S., Mathews, F.S.

To be published.

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: 88.76 kDa 
• Atom Count: 7,300 
• Modeled Residue Count: 770 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monomeric sarcosine oxidase	A, B	389	Bacillus sp. (in: firmicutes)	Mutation(s): 0  Gene Names: soxA, sox EC: 1.5.3.1
UniProt
Find proteins for P40859 (Bacillus sp. (strain B-0618)) Explore P40859  Go to UniProtKB:  P40859

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], M [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FOA	F [auth A], G [auth A], L [auth B], N [auth B]	2-FUROIC ACID C5 H4 O3 SMNDYUVBFMFKNZ-UHFFFAOYSA-N
PO4	D [auth A], J [auth B], K [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H [auth A], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.195 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.177 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.727	α = 90
b = 69.44	β = 94.16
c = 73.671	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Chen, Z., Trickey, P., Jorns, M.S., Mathews, F.S.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2012-03-28
  Changes: Non-polymer description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary