4BJP | pdb_00004bjp

Crystal structure of E. coli penicillin binding protein 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.245 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4BJP

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Penicillin-Binding Protein 3 (Pbp3) from Escherichia Coli.

Sauvage, E.Derouaux, A.Fraipont, C.Joris, M.Herman, R.Rocaboy, M.Schloesser, M.Dumas, J.Kerff, F.Nguyen-Disteche, M.Charlier, P.

(2014) PLoS One 9: 98042

  • DOI: https://doi.org/10.1371/journal.pone.0098042
  • Primary Citation Related Structures: 
    4BJP, 4BJQ

  • PubMed Abstract: 

    In Escherichia coli, penicillin-binding protein 3 (PBP3), also known as FtsI, is a central component of the divisome, catalyzing cross-linking of the cell wall peptidoglycan during cell division. PBP3 is mainly periplasmic, with a 23 residues cytoplasmic tail and a single transmembrane helix. We have solved the crystal structure of a soluble form of PBP3 (PBP3(57-577)) at 2.5 Å revealing the two modules of high molecular weight class B PBPs, a carboxy terminal module exhibiting transpeptidase activity and an amino terminal module of unknown function. To gain additional insight, the PBP3 Val88-Ser165 subdomain (PBP3(88-165)), for which the electron density is poorly defined in the PBP3 crystal, was produced and its structure solved by SAD phasing at 2.1 Å. The structure shows a three dimensional domain swapping with a β-strand of one molecule inserted between two strands of the paired molecule, suggesting a possible role in PBP3(57-577) dimerization.


  • Organizational Affiliation
    • Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5a et Institut de Chimie B6a, Sart Tilman, Liège, Belgium.

Macromolecule Content 

  • Total Structure Weight: 58.1 kDa 
  • Atom Count: 3,409 
  • Modeled Residue Count: 409 
  • Deposited Residue Count: 511 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN511Escherichia coliMutation(s): 0 
EC: 2.4.1.129

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CXS

Query on CXS



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
T [auth A]
U [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
DA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.025α = 90
b = 119.025β = 90
c = 139.251γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description