3V4C

Crystal structure of a semialdehyde dehydrogenase from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb3V4C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-12-14 Released: 2011-12-28 
• Deposition Author(s): Agarwal, R., 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.225 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 

Literature

Crystal structure of a semialdehyde dehydrogenase from Sinorhizobium meliloti 1021

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 113.39 kDa 
• Atom Count: 8,100 
• Modelled Residue Count: 1,004 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase (NADP+)	A, B	528	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: RB0252, SM_b20262 EC: 1.2.1.4
UniProt
Find proteins for Q92WS7 (Rhizobium meliloti (strain 1021)) Explore Q92WS7  Go to UniProtKB:  Q92WS7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	C [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.225 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.197	α = 90
b = 46.079	β = 104.76
c = 117.404	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
ARP/wARP	model building
Coot	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Agarwal, R., 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: 2011-12-28
  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