3NDR | pdb_00003ndr

Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

• PDB DOI: https://doi.org/10.2210/pdb3NDR/pdb

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


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

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.

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: 105.3 kDa 
• Atom Count: 7,384 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.203	α = 90
b = 51.109	β = 89.36
c = 91.732	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-11-13
  Changes: Structure summary