1K6F | pdb_00001k6f

Crystal Structure of the Collagen Triple Helix Model [(Pro-Pro-Gly)10]3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.297 (Depositor) 
  • R-Value Work: 
    0.181 (Depositor) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)(10)](3)

Berisio, R., Vitagliano, L., Mazzarella, L., Zagari, A.

(2002) Protein Sci 11: 262-270

  • DOI: https://doi.org/10.1110/ps.32602
  • Primary Citation Related Structures: 
    1K6F

  • PubMed Abstract: 

    The first report of the full-length structure of the collagen-like polypeptide [(Pro-Pro-Gly)(10)](3) is given. This structure was obtained from crystals grown in a microgravity environment, which diffracted up to 1.3 A, using synchrotron radiation. The final model, which was refined to an R(factor) of 0.18, is the highest-resolution description of a collagen triple helix reported to date. This structure provides clues regarding a series of aspects related to collagen triple helix structure and assembly. The strict dependence of proline puckering on the position inside the Pro-Pro-Gly triplets and the correlation between backbone and side chain dihedral angles support the propensity-based mechanism of triple helix stabilization/destabilization induced by hydroxyproline. Furthermore, the analysis of [(Pro-Pro-Gly)(10)](3) packing, which is governed by electrostatic interactions, suggests that charges may act as locking features in the axial organization of triple helices in the collagen fibrils.

    • Organizational Affiliation: 
    • Centro di Studio di Biocristallografia, CNR, I-80134 Napoli, Italy.

Macromolecule Content 

  • Total Structure Weight: 15.18 kDa 
  • Atom Count: 1,408 
  • Modeled Residue Count: 174 
  • Deposited Residue Count: 180 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
collagen triple helix
A, B, C, D, E
A, B, C, D, E, F
30N/AMutation(s): 0 
UniProt
Find proteins for Q80BK4 (Saimiriine herpesvirus 2)
Explore Q80BK4 
Go to UniProtKB:  Q80BK4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80BK4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.297 (Depositor) 
  • R-Value Work:  0.181 (Depositor) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.907α = 90
b = 26.357β = 90
c = 182.498γ = 90
Software Package:
Software NamePurpose
ARP/wARPmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references, Structure summary
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2024-02-07
    Changes: Data collection, Database references