4H2P

Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO)

• PDB DOI: https://doi.org/10.2210/pdb4H2P/pdb

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


• Deposited: 2012-09-13 Released: 2013-09-18 
• Deposition Author(s): Kobayashi, J., Yoshida, H., Mikami, B., Hayashi, H., Kamitori, S., Yagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.200 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

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

Kobayashi, J., Yoshida, H., Mikami, B., Hayashi, H., Kamitori, S., 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: 178.18 kDa 
• Atom Count: 13,768 
• Modelled Residue Count: 1,481 
• Deposited Residue Count: 1,516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase	A, B, C, D	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	BB [auth C], E [auth A], X [auth B], ZB [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PG4	AB [auth B], XC [auth D], YB [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	W [auth A], ZA [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	Q [auth A], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], TB [auth C], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], WA [auth B], WB [auth C], WC [auth D], XA [auth B], XB [auth C], YA [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	AA [auth B], BA [auth B], BC [auth D], CC [auth D], DB [auth C], DC [auth D], EB [auth C], EC [auth D], FB [auth C], G [auth A], H [auth A], Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	AC [auth D], CB [auth C], F [auth A], Y [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	CA [auth B], DA [auth B], EA [auth B], FA [auth B], FC [auth D], GA [auth B], GB [auth C], GC [auth D], HA [auth B], HB [auth C], HC [auth D], I [auth A], IA [auth B], IB [auth C], IC [auth D], J [auth A], JA [auth B], JB [auth C], JC [auth D], K [auth A], KA [auth B], KB [auth C], KC [auth D], L [auth A], LA [auth B], LB [auth C], LC [auth D], M [auth A], MA [auth B], MB [auth C], MC [auth D], N [auth A], NA [auth B], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], QA [auth B], QB [auth C], QC [auth D], RB [auth C], RC [auth D], SB [auth C], SC [auth D], TC [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.200 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.838	α = 90
b = 103.838	β = 90
c = 452.781	γ = 120

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: 2013-09-18 
Deposition Author(s): Kobayashi, J., Yoshida, H., Mikami, B., Hayashi, H., Kamitori, S., Yagi, T.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description