3HJG

Crystal structure of putative alpha-ribazole-5'-phosphate phosphatase CobC FROM Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3HJG/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-21 Released: 2009-06-02 
• Deposition Author(s): Patskovsky, Y., Toro, R., Morano, C., Rutter, M., Iizuka, M., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Literature

Crystal structure of putative alpha-ribazole-5' -phosphate phosphatase FROM Vibrio parahaemolyticus

Patskovsky, Y., Toro, R., Morano, C., Rutter, M., Iizuka, M., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 48.34 kDa 
• Atom Count: 3,214 
• Modelled Residue Count: 404 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative alpha-ribazole-5'-phosphate phosphatase CobC	A, B	213	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: VP1307 EC: 3.1.3.73
UniProt
Find proteins for Q87Q43 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87Q43  Go to UniProtKB:  Q87Q43

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.215	α = 90
b = 107.215	β = 90
c = 206.717	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Patskovsky, Y., Toro, R., Morano, C., Rutter, M., Iizuka, M., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references