3T37 | pdb_00003t37

Crystal structure of pyridoxine 4-oxidase from Mesorbium loti

• PDB DOI: https://doi.org/10.2210/pdb3T37/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mesorhizobium loti
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-25 Released: 2012-08-15 
• Deposition Author(s): Mugo, A.N., Kobayashi, J., Mikami, B., Ohnishi, K., Yagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.220 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structure biology and crystallization communication

Mugo, A.N., Kobayashi, J., Mikami, B., Ohnishi, K., Yagi, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.4 kDa 
• Atom Count: 4,140 
• Modeled Residue Count: 509 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable dehydrogenase	A	526	Mesorhizobium loti	Mutation(s): 0  Gene Names: mll6785, pno EC: 1.1.3.12
UniProt
Find proteins for Q5NT46 (Rhizobium loti) Explore Q5NT46  Go to UniProtKB:  Q5NT46

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.220 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.38	α = 90
b = 79.438	β = 90
c = 136.429	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Mugo, A.N., Kobayashi, J., Mikami, B., Ohnishi, K., Yagi, T.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Data collection, Experimental preparation
• Version 1.2: 2019-03-13
  Changes: Data collection
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description