3TOX | pdb_00003tox

Crystal structure of a short chain dehydrogenase in complex with NAD(P) from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb3TOX/pdb

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


• Deposited: 2011-09-06 Released: 2011-09-21 
• 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: 1.93 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a short chain dehydrogenase in complex with NAD(P) from Sinorhizobium meliloti 1021

Agarwal, R., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 233.3 kDa 
• Atom Count: 15,313 
• Modeled Residue Count: 2,023 
• Deposited Residue Count: 2,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C, D, E, F, G, H [auth I]	280	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: R00292, SMc00372
UniProt
Find proteins for Q92SS3 (Rhizobium meliloti (strain 1021)) Explore Q92SS3  Go to UniProtKB:  Q92SS3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth I]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.975	α = 90
b = 122.942	β = 90.03
c = 139.818	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
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: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description