3RWB | pdb_00003rwb

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

• PDB DOI: https://doi.org/10.2210/pdb3RWB/pdb

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


• Deposited: 2011-05-08 Released: 2012-05-09 
• Deposition Author(s): Chu, H.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.166 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal 4-dehydrogenase	A, B, C, D	247	Mesorhizobium loti	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], J [auth B], L [auth C], O [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
4PL	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	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), 0.160 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.537	α = 90
b = 50.211	β = 90.47
c = 94.266	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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