4H15 | pdb_00004h15

Crystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P21

• PDB DOI: https://doi.org/10.2210/pdb4H15/pdb

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


• Deposited: 2012-09-10 Released: 2012-09-19 
• Deposition Author(s): Ghosh, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.167 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P21

Ghosh, A., Bhoshle, R., Toro, R., Gizzi, A., Hillerich, B., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium

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: 113.22 kDa 
• Atom Count: 9,061 
• Modeled Residue Count: 1,044 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain alcohol dehydrogenase-related dehydrogenase	A, B, C, D	261	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: RA0888, SMa1629 EC: 1.1.1
UniProt
Find proteins for Q92YJ2 (Rhizobium meliloti (strain 1021)) Explore Q92YJ2  Go to UniProtKB:  Q92YJ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	AB [auth C], IA [auth B], JA [auth B], KA [auth B], NB [auth D], OB [auth D], T [auth A], U [auth A], V [auth A], XA [auth C], YA [auth C], ZA [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	BB [auth D], CB [auth D], DB [auth D], E [auth A], EB [auth D], LA [auth C], MA [auth C], NA [auth C], W [auth B], X [auth B], Y [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], F [auth A], FA [auth B], FB [auth D], G [auth A], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth D], I [auth A], IB [auth D], J [auth A], JB [auth D], K [auth A], KB [auth D], L [auth A], LB [auth D], M [auth A], MB [auth D], N [auth A], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.45 Å
• R-Value Free:  0.167 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.304	α = 90
b = 119.143	β = 105.83
c = 67.156	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Ghosh, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary