3NUG | pdb_00003nug

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

• PDB DOI: https://doi.org/10.2210/pdb3NUG/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

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

• PubMed: 21307574 
• DOI: https://doi.org/10.1271/bbb.100748
• Primary Citation Related Structures: 
  3NUG


• 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 replacement with (S)-1-phenylthanol dehydrogenase (PDB code 2EW8) was adopted to determine the tertiary structure of the NAD(+)-bound enzyme.

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

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: 104.42 kDa 
• Atom Count: 8,371 
• Modeled Residue Count: 988 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-(Acyl-carrier protein) reductase	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], I [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ACY	H [auth C]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.638	α = 90
b = 50.695	β = 89.29
c = 94.551	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2023-11-01
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description