3FKH | pdb_00003fkh

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.287 (Depositor), 0.290 (DCC)
R-Value Work:
0.243 (Depositor), 0.244 (DCC)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative pyridoxamine 5'-phosphate oxidase	A, B, C, D, E 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	3D Interactions
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain M [auth E] SDF format, chain O [auth F] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain M [auth E] MOL2 format, chain O [auth F] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain M [auth E] mmCIF format, chain O [auth F]	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		Interactions Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain O [auth F] Interactions & Density Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain O [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain N [auth E] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E]	J [auth C], L [auth D], N [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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 (Depositor), 0.290 (DCC)
R-Value Work: 0.243 (Depositor), 0.244 (DCC)
R-Value Observed: 0.245 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-01-13

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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
Version 1.5: 2024-11-27
Changes: Data collection, Refinement description, Structure summary