3ALL | pdb_00003all

Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, mutant Y270A

• PDB DOI: https://doi.org/10.2210/pdb3ALL/pdb

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


• Deposited: 2010-08-04 Released: 2011-08-10 
• Deposition Author(s): Kobayashi, J., Yoshida, H., Yoshikane, Y., Kamitori, S., Yagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

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

Kobayashi, J., Yoshida, H., Yoshikane, Y., Kamitori, S., Yagi, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 85.6 kDa 
• Atom Count: 6,279 
• Modeled Residue Count: 741 
• 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 (PDB Primary Data), 1.14.13.242 (UniProt)
UniProt
Find proteins for Q988D3 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q988D3  Go to UniProtKB:  Q988D3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	D [auth A], I [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.085	α = 90
b = 284.981	β = 90
c = 123.683	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Kobayashi, J., Yoshida, H., Yoshikane, Y., Kamitori, S., Yagi, T.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description