4GYM | pdb_00004gym

Crystal structure of Glyoxalase/bleomycin resistance protein/dioxygenase from Conexibacter woesei DSM 14684

• PDB DOI: https://doi.org/10.2210/pdb4GYM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Conexibacter woesei DSM 14684
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-05 Released: 2012-09-26 
• Deposition Author(s): Chang, C., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.187 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Crystal structure of Glyoxalase/bleomycin resistance protein/dioxygenase from Conexibacter woesei DSM 14684

Chang, C., Tesar, C., Clancy, S., Joachimiak, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.2 kDa 
• Atom Count: 2,513 
• Modeled Residue Count: 283 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B	149	Conexibacter woesei DSM 14684	Mutation(s): 0  Gene Names: Cwoe_2487
UniProt
Find proteins for D3F7P7 (Conexibacter woesei (strain DSM 14684 / CCUG 47730 / CIP 108061 / JCM 11494 / NBRC 100937 / ID131577)) Explore D3F7P7  Go to UniProtKB:  D3F7P7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.56 Å
• R-Value Free:  0.187 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GYM

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.943	α = 90
b = 58.943	β = 90
c = 164.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Chang, C., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary