2RK9 | pdb_00002rk9

The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01

• PDB DOI: https://doi.org/10.2210/pdb2RK9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio splendidus 12B01
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-10-16 Released: 2007-10-30 
• Deposition Author(s): Tyagi, R., Eswaramoorthy, S., Sauder, J.M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01.

Tyagi, R., Eswaramoorthy, S., Sauder, J.M., Burley, S.K., Swaminathan, S.

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: 33.71 kDa 
• Atom Count: 2,123 
• Modeled Residue Count: 233 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B	145	Vibrio splendidus 12B01	Mutation(s): 1  Gene Names: 84385607, V12B01_25774

Small Molecules

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: 1.60 Å
• R-Value Free:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.704	α = 90
b = 76.954	β = 92
c = 42.395	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Tyagi, R., Eswaramoorthy, S., Sauder, J.M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary