7E2A

GDPD mutant from Pyrococcus furiosus DSM 3638

• PDB DOI: https://doi.org/10.2210/pdb7E2A/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-02-05 Released: 2022-02-09 
• Deposition Author(s): Wang, Y.H., Wang, J., Wang, F.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Crystal structure of glycerophoshphodiester phospodiesterase D60A mutant from Pyrococcus furiosus DSM

Wang, Y.H., Wang, J., Wang, F.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.37 kDa 
• Atom Count: 2,108 
• Modelled Residue Count: 253 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphodiester phosphodiesterase	A	255	Pyrococcus furiosus DSM 3638	Mutation(s): 1  Gene Names: PF2003
UniProt
Find proteins for Q8TZI9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZI9  Go to UniProtKB:  Q8TZI9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.89	α = 90
b = 69.6	β = 90
c = 89.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Wang, Y.H., Wang, J., Wang, F.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31725022
National Natural Science Foundation of China (NSFC)	China	31972014

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description