1V8E | pdb_00001v8e

Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1V8E/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-05 Released: 2005-01-18 
• Deposition Author(s): Ishijima, J., Ida, K., Yutani, K., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal structure of glycerophosphoryl diester phosphodiesterase from Thermus thermophilus HB8

Ishijima, J., Ida, K., Yutani, K., Miyano, M.

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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 24.44 kDa 
• Atom Count: 1,955 
• Modeled Residue Count: 217 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative glycerophosphoryl diester phosphodiesterase	A	224	Thermus thermophilus HB8	Mutation(s): 0  EC: 3.1.4.46
UniProt
Find proteins for Q53W25 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W25  Go to UniProtKB:  Q53W25

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.221	α = 90
b = 74.221	β = 90
c = 73.518	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Ishijima, J., Ida, K., Yutani, K., Miyano, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references
• Version 1.4: 2024-10-16
  Changes: Structure summary