1OAP | pdb_00001oap

Mad structure of the periplasmique domain of the Escherichia coli PAL protein

• PDB DOI: https://doi.org/10.2210/pdb1OAP/pdb

• Classification: LIPOPROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-01-20 Released: 2004-02-13 
• Deposition Author(s): Abergel, C., Walburger, A., Bouveret, E., Claverie, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystallization and preliminary crystallographic study of the peptidoglycan-associated lipoprotein from Escherichia coli.

Abergel, C., Walburger, A., Chenivesse, S., Lazdunski, C.

(2001) Acta Crystallogr D Biol Crystallogr 57: 317-319

• PubMed: 11173492 
• DOI: https://doi.org/10.1107/s0907444900019739
• Primary Citation Related Structures: 
  1OAP


• PubMed Abstract: 
  

  The peptidoglycan-associated lipoprotein (Pal) from Escherichia coli is part of the Tol--Pal multiprotein complex used by group A colicins to penetrate and kill cells. Pal homologues are found in many Gram-negative bacteria and the Tol--Pal system is thought to play a role in bacterial envelope integrity. The Pal protein comprises 152 amino acids. Crystals of the C-terminal 109-amino-acid fragment of the Pal protein have been produced. The crystals belong to the tetragonal space group I4(1), with unit-cell parameters a = b = 89.3, c = 67.2 A. There are two molecules in the asymmetric unit. Frozen crystals diffract to at least 2.8 A resolution using synchrotron radiation. Selenomethionine-substituted truncated Pal protein is currently being produced in order to use multiwavelength anomalous dispersion (MAD) for phasing.

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Organizational Affiliation: 
• Information Génétique et Structurale, UMR1889 CNRS-AVENTIS, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 12.51 kDa 
• Atom Count: 956 
• Modeled Residue Count: 108 
• Deposited Residue Count: 109 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN	A	109	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A912 (Escherichia coli (strain K12)) Explore P0A912  Go to UniProtKB:  P0A912

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.575	α = 90
b = 88.575	β = 90
c = 68.028	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-13 
Deposition Author(s): Abergel, C., Walburger, A., Bouveret, E., Claverie, J.M.

Revision History  

• Version 1.0: 2004-02-13
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
• Version 1.2: 2018-03-28
  Changes: Source and taxonomy
• Version 1.3: 2019-10-09
  Changes: Data collection, Database references, Other
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations