2EXA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DGF
Query on DGF

Download SDF File 
Download CCD File 
A
(2R,5R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid
FAROPENEM PRODUCT, BOUND FORM
C12 H17 N O5 S
FHQOUTNMKXYVEY-MKSGQPMJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.627α = 90.00
b = 95.627β = 90.00
c = 115.647γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

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: Non-polymer description, Version format compliance
  • Version 1.3: 2012-10-31
    Type: Advisory, Non-polymer description
  • Version 1.4: 2016-10-19
    Type: Database references, Non-polymer description