4H2R | pdb_00004h2r

Structure of MHPCO Y270F mutant, 5-hydroxynicotinic acid complex

• PDB DOI: https://doi.org/10.2210/pdb4H2R/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mesorhizobium japonicum MAFF 303099
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.47 Å
• R-Value Free: 
  0.261 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

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: 85.81 kDa 
• Atom Count: 5,961 
• Modeled Residue Count: 738 
• Deposited Residue Count: 758 
• 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	379	Mesorhizobium japonicum MAFF 303099	Mutation(s): 1  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	C [auth A], I [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
5HN	E [auth A]	5-hydroxypyridine-3-carboxylic acid C6 H5 N O3 ATTDCVLRGFEHEO-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.261 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.891	α = 90
b = 284.553	β = 90
c = 125.001	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: 2013-09-18 
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