2JB4 | pdb_00002jb4

Isopenicillin N synthase with a 2-thiabicycloheptan-6-one product analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.176 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2JB4

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

A Cyclobutanone Analogue Mimics Penicillin in Binding to Isopenicillin N Synthase.

Stewart, A.C.Clifton, I.J.Adlington, R.M.Baldwin, J.E.Rutledge, P.J.

(2007) Chembiochem 8: 2003

  • DOI: https://doi.org/10.1002/cbic.200700176
  • Primary Citation Related Structures: 
    2JB4

  • PubMed Abstract: 

    A carbocyclic analogue of the beta-lactam antibiotic isopenicillin N (IPN) has been synthesised and cocrystallised with isopenicillin N synthase (IPNS), the central enzyme in the biosynthesis of penicillin antibiotics. The crystal structure of the IPNS-cyclobutanone complex reveals an active site environment similar to that seen in the enzyme-product complex generated by turnover of the natural substrate within the crystalline protein. The IPNS-cyclobutanone structure demonstrates that the product analogue is tethered to the protein by hydrogen bonding and salt bridge interactions with its carboxylate groups, as seen previously for the natural substrate and product. Furthermore, the successful cocrystallisation of this analogue with IPNS provides firm structural evidence for the utility of such cyclobutanone derivatives as hydrolytically stable analogues of bicyclic beta-lactams.


  • Organizational Affiliation
    • Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.

Macromolecule Content 

  • Total Structure Weight: 38.26 kDa 
  • Atom Count: 3,096 
  • Modeled Residue Count: 329 
  • Deposited Residue Count: 331 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isopenicillin N synthase331Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: ipnAipsAN2622
EC: 1.21.3.1
UniProt
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P05326 
Go to UniProtKB:  P05326
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05326
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A14

Query on A14



Download:Ideal Coordinates CCD File
B [auth A](1S,4S,5S,7R)-7-{[(5S)-5-AMINO-5-CARBOXYPENTANOYL]AMINO}-3,3-DIMETHYL-6-OXO-2-THIABICYCLO[3.2.0]HEPTANE-4-CARBOXYLIC ACID
C15 H22 N2 O6 S
FIHUDIADLMVJET-CEAFUOJOSA-N
SO4

Query on SO4



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

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.176 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.677α = 90
b = 71.273β = 90
c = 100.906γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-05-08
    Changes: Database references, Source and taxonomy, Structure summary