2EX8

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with penicillin-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics

Kishida, H.Unzai, S.Roper, D.I.Lloyd, A.Park, S.-Y.Tame, J.R.H.

(2006) Biochemistry 45: 783-792

  • DOI: 10.1021/bi051533t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented. PBP4 is one of 12 penicillin binding proteins in E. coli involved in the synthesis and ...

    The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented. PBP4 is one of 12 penicillin binding proteins in E. coli involved in the synthesis and maintenance of the cell wall. The model contains a penicillin binding domain similar to known structures, but includes a large insertion which folds into domains with unique folds. The structures of the protein covalently attached to five different antibiotics presented here show the active site residues are unmoved compared to the apoprotein, but nearby surface loops and helices are displaced in some cases. The altered geometry of conserved active site residues compared with those of other PBPs suggests a possible cause for the slow deacylation rate of PBP4.


    Organizational Affiliation

    Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Penicillin-binding protein 4
A
458Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: dacB
EC: 3.4.16.4
Find proteins for P24228 (Escherichia coli (strain K12))
Go to UniProtKB:  P24228
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNM
Query on PNM

Download SDF File 
Download CCD File 
A
OPEN FORM - PENICILLIN G
C16 H20 N2 O4 S
OGFZUTGOGYUTKZ-KWCYVHTRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.867α = 90.00
b = 95.867β = 90.00
c = 116.159γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2016-10-19
    Type: Database references