2EX9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 

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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: https://doi.org/10.1021/bi051533t
  • Primary Citation of Related Structures:  
    2EX2, 2EX6, 2EX8, 2EX9, 2EXA, 2EXB

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 4458Escherichia coliMutation(s): 1 
Gene Names: dacB
EC: 3.4.16.4 (PDB Primary Data), 3.4.99 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for P24228 (Escherichia coli (strain K12))
Explore P24228 
Go to UniProtKB:  P24228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24228
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
35P
Query on 35P

Download Ideal Coordinates CCD File 
B [auth A](2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenoxyacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid
C16 H20 N2 O5 S
OQVOJWZOUWGSDX-KWCYVHTRSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.758α = 90
b = 95.758β = 90
c = 115.878γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 35PClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2016-10-19
    Changes: Database references, Non-polymer description
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary