3ZVS

Crystal structure of Archaemetzincin (AmzA) from Archaeoglobus fulgidus at 1.4 A resolution complexed with malonate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Crystal Structures of Archaemetzincin Reveal a Moldable Substrate-Binding Site.

Graef, C., Schacherl, M., Waltersperger, S., Baumann, U.

(2012) PLoS One 7: 43863

  • DOI: https://doi.org/10.1371/journal.pone.0043863
  • Primary Citation of Related Structures:  
    3ZVS, 4A3W, 4AXQ

  • PubMed Abstract: 

    Archaemetzincins are metalloproteases occurring in archaea and some mammalia. They are distinct from all the other metzincins by their extended active site consensus sequence HEXXHXXGXXHCX(4)CXMX(17)CXXC featuring four conserved cysteine residues. Very little is known about their biological importance and structure-function relationships.

    • Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ARCHAEMETZINCIN
A, B, C
160Archaeoglobus fulgidusMutation(s): 0 
EC: 3
UniProt
Find proteins for O29917 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29917 
Go to UniProtKB:  O29917
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29917
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
M [auth C]		MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
H [auth B]
I [auth B]
K [auth C]
D [auth A],
E [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.302α = 71.39
b = 63.49β = 86.68
c = 64.533γ = 82.67
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-09-12
    Changes: Database references, Other
  • Version 2.0: 2023-12-20
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description