4GF7

Crystal structure of 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO), unliganded form

• PDB DOI: https://doi.org/10.2210/pdb4GF7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mesorhizobium japonicum MAFF 303099
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-03 Released: 2013-08-07 
• Deposition Author(s): Kobayashi, J., Yoshida, H., Mikami, B., Hayashi, H., Kamitori, S., Sawa, Y., Yagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.192 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase

Kobayashi, J., Yoshida, H., Mikami, B., Hayashi, H., Kamitori, S., Sawa, Y., Yagi, T.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.23 kDa 
• Atom Count: 3,474 
• Modelled Residue Count: 370 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase	A	379	Mesorhizobium japonicum MAFF 303099	Mutation(s): 0  Gene Names: mlr6788 EC: 1.14.12.4
UniProt
Find proteins for Q988D3 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q988D3  Go to UniProtKB:  Q988D3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEG	I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	C [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.192 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.363	α = 90
b = 131.287	β = 90
c = 132.289	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Kobayashi, J., Yoshida, H., Mikami, B., Hayashi, H., Kamitori, S., Sawa, Y., Yagi, T.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description