3FKH

Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.51 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3FKH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-16 Released: 2009-01-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.287 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Literature

Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.51 A resolution

Joint Center for Structural Genomics (JCSG)

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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.87 kDa 
• Atom Count: 6,187 
• Modelled Residue Count: 773 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative pyridoxamine 5'-phosphate oxidase	A, B, C, D, E, F	138	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: cg2794, NP_601736.1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	G [auth B], I [auth C], K [auth D], M [auth E], O [auth F]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
GOL	J [auth C], L [auth D], N [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	H [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.287 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M33FKH

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.63	α = 90
b = 88.31	β = 90
c = 138.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations, Structure summary