2KNT

THE 1.2 ANGSTROM STRUCTURE OF KUNITZ TYPE DOMAIN C5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

1.2 A refinement of the Kunitz-type domain from the alpha3 chain of human type VI collagen.

Merigeau, K.Arnoux, B.Perahia, D.Norris, K.Norris, F.Ducruix, A.

(1998) Acta Crystallogr.,Sect.D 54: 306-312


  • PubMed Abstract: 
  • The recombinant Kunitz-type domain (C5) of human collagen alpha3(VI) chain was previously described at 1.6 A resolution at room temperature. By changing the crystallization conditions and using synchrotron radiation, we are able to record diffraction ...

    The recombinant Kunitz-type domain (C5) of human collagen alpha3(VI) chain was previously described at 1.6 A resolution at room temperature. By changing the crystallization conditions and using synchrotron radiation, we are able to record diffraction data to 1.2 A resolution for crystals of the same space group at 291 K. The protein-water-ion model has been refined anisotropically against these new data using the program SHELXL93; the results converged to an R factor of 15.0%, with all data between 7 and 1.2 A. The final electron-density map reveals a clear chain tracing with a few disordered residues and five residues out of 58 that present alternate conformations. The Cys14-Cys38 bond presents the less frequently observed left-hand conformation (chi1 = -60 degrees). The solvent molecules and a phosphate ion are well ordered with an average B of 38 A2. The high-resolution structure reveals the N and C termini which were missing from the 1.6 A structure.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 91198 Gif sur Yvette CEDEX, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLLAGEN
A
58Homo sapiensMutation(s): 0 
Gene Names: COL6A3
Find proteins for P12111 (Homo sapiens)
Go to Gene View: COL6A3
Go to UniProtKB:  P12111
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 25.690α = 90.00
b = 38.040β = 109.20
c = 28.640γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
AGROVATAdata reduction
AGROVATAdata scaling
SHELXL-93refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-05-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance