7E0V

GDPD from Pyrococcus furiosus DSM 3638

• PDB DOI: https://doi.org/10.2210/pdb7E0V/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-28 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: 1.65 Å
• R-Value Free: 0.192 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

Crystal structure of Bomgl, a monoacylglycerol lipase from marine Bacillus

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.84 kDa 
• Atom Count: 4,481 
• Modelled Residue Count: 504 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphodiester phosphodiesterase	A, B [auth C]	255	Pyrococcus furiosus DSM 3638	Mutation(s): 0  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: 1.65 Å
• R-Value Free: 0.192 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.33	α = 90
b = 45.87	β = 109.144
c = 96.66	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