3U4J

Crystal structure of NAD-dependent aldehyde dehydrogenase from Sinorhizobium meliloti

• PDB DOI: https://doi.org/10.2210/pdb3U4J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-10-08 Released: 2011-10-19 
• Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Crystal structure of NAD-dependent aldehyde dehydrogenase from Sinorhizobium meliloti

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

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: 229.11 kDa 
• Atom Count: 15,736 
• Modelled Residue Count: 2,015 
• Deposited Residue Count: 2,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent aldehyde dehydrogenase	A, B, C, D	528	Sinorhizobium meliloti	Mutation(s): 0  Gene Names: RA0117, SMa0220
UniProt
Find proteins for Q930S8 (Rhizobium meliloti (strain 1021)) Explore Q930S8  Go to UniProtKB:  Q930S8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-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: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.108	α = 90
b = 176.66	β = 98.49
c = 83.662	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection