3NUG

Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.788 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti

Chu, H.N.Kobayashi, J.Mikami, B.Yagi, T.

(2011) Biosci.Biotechnol.Biochem. 75: 388-390

  • DOI: 10.1271/bbb.100748

  • PubMed Abstract: 
  • Pyridoxal 4-dehydrogenase catalyzes the irreversible oxidation of pyridoxal to 4-pyridoxolactone and is involved in degradation pathway I of pyridoxine, a vitamin B(6) compound. Its crystal structure was elucidated for the first time. Molecular repla ...

    Pyridoxal 4-dehydrogenase catalyzes the irreversible oxidation of pyridoxal to 4-pyridoxolactone and is involved in degradation pathway I of pyridoxine, a vitamin B(6) compound. Its crystal structure was elucidated for the first time. Molecular replacement with (S)-1-phenylthanol dehydrogenase (PDB code 2EW8) was adopted to determine the tertiary structure of the NAD(+)-bound enzyme.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti.
      Chu, H.N.,Kobayashi, J.,Yoshikane, Y.,Mikami, B.,Yagi, T.
      (2010) Acta Crystallogr.,Sect.F 66: 718


    Organizational Affiliation

    Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-oxoacyl-(Acyl-carrier protein) reductase
A, B, C, D
247Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)Mutation(s): 0 
Gene Names: pldh-t
EC: 1.1.1.107
Find proteins for Q988B7 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099))
Go to UniProtKB:  Q988B7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
C
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.788 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.638α = 90.00
b = 50.695β = 89.29
c = 94.551γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-07-06 
  • Released Date: 2011-04-20 
  • Deposition Author(s): Chu, H.N.

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description