1M4L

STRUCTURE OF NATIVE CARBOXYPEPTIDASE A AT 1.25 RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.104 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Refined structure of bovine carboxypeptidase A at 1.25 A resolution.

Kilshtain-Vardi, A.Glick, M.Greenblatt, H.M.Goldblum, A.Shoham, G.

(2003) Acta Crystallogr D Biol Crystallogr 59: 323-333

  • DOI: https://doi.org/10.1107/s0907444902015706
  • Primary Citation of Related Structures:  
    1M4L

  • PubMed Abstract: 

    The crystal structure of the bovine zinc metalloproteinase carboxypeptidase A (CPA) has been refined to 1.25 A resolution based on room-temperature X-ray synchrotron data. The significantly improved structure of CPA at this resolution (anisotropic temperature factors, R factor = 10.4%, R(free) = 14.5%) allowed the modelling of conformational disorders of side chains, improved the description of the protein solvent network (375 water molecules) and provided a more accurate picture of the interactions between the active-site zinc and its ligands. The calculation of standard uncertainties in individual atom positions of the refined model of CPA allowed the deduction of the protonation state of some key residues in the active site and confirmed that Glu72 and Glu270 are negatively charged in the resting state of the enzyme at pH 7.5. These results were further validated by theoretical calculations that showed significant reduction of the pK(a) of these side chains relative to solution values. The distance between the zinc-bound solvent molecule and the metal ion is strongly suggestive of a neutral water molecule and not a hydroxide ion in the resting state of the enzyme. These findings could support both the general acid/general base mechanism, as well as the anhydride mechanism suggested for CPA.


  • Organizational Affiliation

    Department of Inorganic Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CARBOXYPEPTIDASE A307Bos taurusMutation(s): 0 
EC: 3.4.17.1
UniProt
Find proteins for P00730 (Bos taurus)
Explore P00730 
Go to UniProtKB:  P00730
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00730
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.104 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.687α = 90
b = 60.267β = 97.47
c = 47.453γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
SHELXL-97refinement
TNTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-10
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description