2CUO

Collagen model peptide (PRO-PRO-GLY)9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Repetitive interactions observed in the crystal structure of a collagen-model peptide, [(Pro-Pro-Gly)9]3

Hongo, C.Noguchi, K.Okuyama, K.Tanaka, Y.Nishino, N.

(2005) J Biochem 138: 135-144

  • DOI: 10.1093/jb/mvi108
  • Primary Citation of Related Structures:  
    2CUO

  • PubMed Abstract: 
  • The crystal structure of a collagen-model peptide [(Pro-Pro-Gly)(9)](3) has been determined at 1.33 A resolution. Diffraction data were collected at 100 K using synchrotron radiation, which led to the first structural study of [(Pro-Pro-Gly)(n)](3) u ...

    The crystal structure of a collagen-model peptide [(Pro-Pro-Gly)(9)](3) has been determined at 1.33 A resolution. Diffraction data were collected at 100 K using synchrotron radiation, which led to the first structural study of [(Pro-Pro-Gly)(n)](3) under cryogenic conditions. The crystals belong to the P2(1) space group with cell parameters of a = 25.95, b = 26.56, c = 80.14 Angstroms and beta = 90.0 degrees. The overall molecular conformation was consistent with the left-handed 7/2-helical model with an axial repeat of 20 A for native collagen. A total of 332 water molecules were found in an asymmetric unit. Proline residues in adjacent triple-helices exhibited three types of hydrophobic interactions. Furthermore, three types of hydrogen-bonding networks mediated by water molecules were observed between adjacent triple-helices. These hydrophobic interactions and hydrogen-bonding networks occurred at intervals of 20 Angstroms along the c-axis based on the previous sub-cell structures [(Pro-Pro-Gly)(n)](3) (n = 9, 10), which were also seen in the full-cell structure of [(Pro-Pro-Gly)(10)](3). Five proline residues at the Y position in the X-Y-Gly triplet were found in a down-puckering conformation, this being inconsistent with the recently proposed propensity-based hypothesis. These proline residues were forced to adopt opposing puckering because of the prevailing hydrophobic interaction between triple-helices compared with the Pro:Pro stacking interaction within a triple-helix.


    Organizational Affiliation

    Faculty of Technology, Tokyo University of Agriculture & Technology, Koganei.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9A, B, C, D, E, F27N/AMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.946α = 90
b = 26.563β = 90
c = 80.14γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
SHELXmodel building
SHELXL-97refinement
CrystalCleardata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance