3VCX | pdb_00003vcx

Crystal structure of a putative glyoxalase/bleomycin resistance protein from Rhodopseudomonas palustris CGA009

• PDB DOI: https://doi.org/10.2210/pdb3VCX/pdb
• Entry: 3VCX supersedes: 3M2O

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-04 Released: 2012-01-18 
• Deposition Author(s): Stogios, P.J., Chang, C., Evdokimova, E., Egorova, O., Joachimiak, A., Edwards, A.M., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.186 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Crystal structure of a putative glyoxalase/bleomycin resistance protein from Rhodopseudomonas palustris CGA009

Stogios, P.J., Chang, C., Evdokimova, E., Egorova, O., Joachimiak, A., Edwards, A.M., Savchenko, A.

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.

Macromolecule Content

• Total Structure Weight: 37.85 kDa 
• Atom Count: 2,328 
• Modelled Residue Count: 242 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/Bleomycin resistance protein/dioxygenase domain	A, B	164	Rhodopseudomonas palustris CGA009	Mutation(s): 0  Gene Names: RPA0902
UniProt
Find proteins for Q6NBC6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NBC6  Go to UniProtKB:  Q6NBC6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-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: 1.39 Å
• R-Value Free:  0.186 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.825	α = 90
b = 67.918	β = 90
c = 103.481	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Stogios, P.J., Chang, C., Evdokimova, E., Egorova, O., Joachimiak, A., Edwards, A.M., Savchenko, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 3M2O

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2012-01-25
  Changes: Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary