3IV6 | pdb_00003iv6

Crystal Structure of Putative Zn-dependent Alcohol Dehydrogenases from Rhodobacter sphaeroides.

• PDB DOI: https://doi.org/10.2210/pdb3IV6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cereibacter sphaeroides 2.4.1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-08-31 Released: 2009-09-15 
• Deposition Author(s): Kim, Y., Marshall, N., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.238 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal Structure of Putative Zn-dependent Alcohol Dehydrogenases from Rhodobacter sphaeroides.

Kim, Y., Marshall, N., Keigher, L., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119.53 kDa 
• Atom Count: 8,466 
• Modeled Residue Count: 1,016 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Zn-dependent Alcohol Dehydrogenase	A, B, C, D	261	Cereibacter sphaeroides 2.4.1	Mutation(s): 0  Gene Names: RHOS4_40580, RSP_4162
UniProt
Find proteins for Q3IV08 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IV08  Go to UniProtKB:  Q3IV08

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	E [auth A], F [auth B], I [auth C], J [auth D]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
CL	G [auth B], H [auth B], K [auth D], L [auth D]	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: 2.70 Å
• R-Value Free:  0.238 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.883	α = 90
b = 179.883	β = 90
c = 83.826	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Kim, Y., Marshall, N., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary