8BM3 | pdb_00008bm3

H207A mutant of E. coli PgpB, a PAP2 type phosphatidyl glycerol phosphate and C55-PP phosphatase, in complex with farnesyl pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb8BM3/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2022-11-10 Released: 2023-11-22 
• Deposition Author(s): Delbrassine, F., El Ghachi, M., Lambion, A., Herman, R., Kerff, F.
• Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

H207A mutant of E. coli PgpB, a PAP2 type phosphatidyl glycerol phosphate and C55-PP phosphatase, in complex with farnesyl pyrophosphate

Delbrassine, F., El Ghachi, M., Lambion, A., Herman, R., Kerff, F.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 122.58 kDa 
• Atom Count: 7,808 
• Modeled Residue Count: 956 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylglycerophosphatase B	A, B, C, D	264	Escherichia coli K-12	Mutation(s): 1  Gene Names: pgpB, b1278, JW1270 EC: 3.1.3.27 (PDB Primary Data), 3.1.3.81 (PDB Primary Data), 3.1.3.4 (PDB Primary Data), 3.6.1.27 (PDB Primary Data), 3.6.1.75 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P0A924 (Escherichia coli (strain K12)) Explore P0A924  Go to UniProtKB:  P0A924

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.273 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.72	α = 90
b = 61.62	β = 90.07
c = 144.24	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Delbrassine, F., El Ghachi, M., Lambion, A., Herman, R., Kerff, F.

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Funding Organization	Location	Grant Number
Fonds National de la Recherche Scientifique (FNRS)	Belgium	MIS 6983808
Fonds National de la Recherche Scientifique (FNRS)	Belgium	PDR-40008487

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release