3RWB | pdb_00003rwb

Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal 4-dehydrogenase) from Mesorhizobium loti

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.166 (Depositor), 0.165 (DCC) 
  • R-Value Work: 
    0.135 (Depositor), 0.133 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal 4-dehydrogenase) from Mesorhizobium loti

Yagi, T., Chu, H.N.

To be published.

Macromolecule Content 

  • Total Structure Weight: 105.48 kDa 
  • Atom Count: 8,559 
  • Modeled Residue Count: 988 
  • Deposited Residue Count: 988 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyridoxal 4-dehydrogenase
A, B, C, D
247Mesorhizobium lotiMutation(s): 0 
Gene Names: mlr6807, pldh-t
EC: 1.1.1.107
UniProt
Find proteins for Q988B7 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099))
Explore Q988B7 
Go to UniProtKB:  Q988B7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ988B7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD


Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
L [auth C],
O [auth D]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
4PL

Query on 4PL


Download:Ideal Coordinates CCD File
F [auth A],
K [auth B],
M [auth C],
P [auth D]		7-hydroxy-6-methylfuro[3,4-c]pyridin-1(3H)-one
C8 H7 N O3
HHPDVQLBYQFYFA-UHFFFAOYSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
N [auth C],
Q [auth D]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.166 (Depositor), 0.165 (DCC) 
  • R-Value Work:  0.135 (Depositor), 0.133 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.537α = 90
b = 50.211β = 90.47
c = 94.266γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2012-05-09 
    • Deposition Author(s): Chu, H.N.

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description