3BG2 | pdb_00003bg2

Crystal structure of deoxyguanosinetriphosphate triphosphohydrolase from Flavobacterium sp. MED217

• PDB DOI: https://doi.org/10.2210/pdb3BG2/pdb

• Classification: HYDROLASE
• Organism(s): Leeuwenhoekiella blandensis MED217
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-25 Released: 2007-12-04 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Meyer, A.J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.285 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.265 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Literature

Crystal structure of the deoxyguanosinetriphosphate triphosphohydrolase from Flavobacterium sp. MED217.

Fedorov, A.A., Fedorov, E.V., Toro, R., Meyer, A.J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 100.94 kDa 
• Atom Count: 6,474 
• Modeled Residue Count: 794 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DGTP triphosphohydrolase	A, B	444	Leeuwenhoekiella blandensis MED217	Mutation(s): 0  Gene Names: MED217_16760
UniProt
Find proteins for A3XHN1 (Leeuwenhoekiella blandensis (strain CECT 7118 / CCUG 51940 / KCTC 22103 / MED217)) Explore A3XHN1  Go to UniProtKB:  A3XHN1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.285 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.265 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.403	α = 90
b = 200.403	β = 90
c = 86.239	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Meyer, A.J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-12-04
  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, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references