3NDR

Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

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

To be published.

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 1 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.203α = 90.00
b = 51.109β = 89.36
c = 91.732γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-06-08 
  • Released Date: 2011-06-08 
  • Deposition Author(s): Chu, H.N.

Revision History 

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance