4UAM

1.8 Angstrom crystal structure of IMP-1 metallo-beta-lactamase with a mixed iron-zinc center in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Iron(III) Located in the Dinuclear Metallo-beta-Lactamase IMP-1 by Pseudocontact Shifts.

Carruthers, T.J.Carr, P.D.Loh, C.T.Jackson, C.J.Otting, G.

(2014) Angew Chem Int Ed Engl 53: 14269-14272

  • DOI: https://doi.org/10.1002/anie.201408693
  • Primary Citation of Related Structures:  
    4UAM

  • PubMed Abstract: 

    Heterodinuclear metalloenzymes are an important class of metalloproteins, but determining the location of the different metal ions can be difficult. Herein we present a new NMR spectroscopy method that uses pseudocontact shifts (PCS) to achieve this without assumptions about the coordinating ligands. The approach is illustrated with the dinuclear [FeZn] complex of IMP-1, which is a prototypical metallo-β-lactamase (MβL) that confers resistance to β-lactam antibiotics. Results from single-crystal X-ray diffraction were compromised by degradation during crystallization. With [GaZn]-IMP-1 as diamagnetic reference, the PCSs unambiguously identified the iron binding site in fresh samples of [FeZn]-IMP-1, even though the two metal centers are less than 3.8 Å apart and the iron is high-spin Fe(3+), which produces only small PCSs. [FeZn]-MβLs may be important drug targets, as [FeZn]-IMP-1 is enzymatically active and readily produced in the presence of small amounts of Fe(3+).


  • Organizational Affiliation

    Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMP-1 metallo-beta-lactamase
A, B, C, D
228Pseudomonas aeruginosa NCGM2.S1Mutation(s): 1 
Gene Names: bla IMPNCGM2_1757
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.99α = 83.45
b = 75.91β = 75.3
c = 82.36γ = 74.01
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2014-12-24
    Changes: Database references
  • Version 1.4: 2017-08-23
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.5: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description