3T37

Crystal structure of pyridoxine 4-oxidase from Mesorbium loti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure biology and crystallization communication

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable dehydrogenase526Mesorhizobium lotiMutation(s): 0 
Gene Names: mll6785pno
EC: 1.1.3.12
UniProt
Find proteins for Q5NT46 (Rhizobium loti)
Explore Q5NT46 
Go to UniProtKB:  Q5NT46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5NT46
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.38α = 90
b = 79.438β = 90
c = 136.429γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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