6NC5

Cronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lactamse HARLDQ motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6DQH


Literature

Broad spectrum antibiotic-degrading metallo-beta-lactamases are phylogenetically diverse.

Pedroso, M.M.Waite, D.W.Melse, O.Wilson, L.Mitic, N.McGeary, R.P.Antes, I.Guddat, L.W.Hugenholtz, P.Schenk, G.

(2020) Protein Cell 11: 613-617


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase260Cronobacter sakazakiiMutation(s): 2 
Gene Names: CSK29544_03680
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
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.468α = 90
b = 74.946β = 90
c = 76.095γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data reduction
PHENIXphasing
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP108477
Australian Research Council (ARC)AustraliaDP150104358
Australian Research Council (ARC)AustraliaT120100694

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 1.2: 2020-07-01
    Changes: Database references
  • Version 1.3: 2020-08-05
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description