7E2B | pdb_00007e2b

GDPD mutant complex from Pyrococcus furiosus DSM 3638

• PDB DOI: https://doi.org/10.2210/pdb7E2B/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli K-12
• 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: 1.85 Å
• R-Value Free: 
  0.220 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Observation of the GPC production during hydrolysis of LPC by GDPD D60A from Pyrococcus furiosus DSM 3638

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.76 kDa 
• Atom Count: 2,201 
• Modeled 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM (Subject of Investigation/LOI)	B [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
CHT (Subject of Investigation/LOI)	C [auth A]	CHOLINE ION C5 H14 N O OEYIOHPDSNJKLS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.220 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.92	α = 90
b = 70.12	β = 90
c = 90.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	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