4OEC | pdb_00004oec

Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1

• PDB DOI: https://doi.org/10.2210/pdb4OEC/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-13 Released: 2015-01-14 
• Deposition Author(s): Atsuta, Y., You, D.J., Takano, K., Koga, Y., Kanaya, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1

Atsuta, Y., You, D.J., Takano, K., Koga, Y., Kanaya, S.

To be published.

Biological Assembly 1  

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

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 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 114.32 kDa 
• Atom Count: 8,713 
• Modeled Residue Count: 992 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphoryl diester phosphodiesterase	A, B, C, D	248	Thermococcus kodakarensis KOD1	Mutation(s): 0  Gene Names: TK1397 EC: 3.1.4.46
UniProt
Find proteins for Q5JGZ3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGZ3  Go to UniProtKB:  Q5JGZ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.724	α = 90
b = 132.034	β = 90
c = 171.639	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Atsuta, Y., You, D.J., Takano, K., Koga, Y., Kanaya, S.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description