1VD6 | pdb_00001vd6

Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase complexed with Glycerol

• PDB DOI: https://doi.org/10.2210/pdb1VD6/pdb

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


• Deposited: 2004-03-18 Released: 2005-04-05 
• Deposition Author(s): Ishijima, J., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase complexed with Glycerol

Ishijima, J., Yutani, K.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 24.53 kDa 
• Atom Count: 2,029 
• Modeled Residue Count: 218 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.194	α = 90
b = 74.194	β = 90
c = 73.439	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-05 
Deposition Author(s): Ishijima, J., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-04-05
  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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary