1V4F

Crystal structures of collagen model peptides with pro-hyp-gly sequence at 1.3A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.133 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: implications for proline ring puckering

Okuyama, K.Hongo, C.Fukushima, R.Wu, G.Narita, H.Noguchi, K.Tanaka, Y.Nishino, N.

(2004) Biopolymers 76: 367-377

  • DOI: https://doi.org/10.1002/bip.20107
  • Primary Citation of Related Structures:  
    1V4F, 1V6Q, 1V7H

  • PubMed Abstract: 

    Triple-helical structures of (Pro-Hyp-Gly)n (n = 10, 11) at 100 K and room temperature (RT) were analyzed at 1.26 A resolution by using synchrotron radiation data. Totals of 49 and 42 water molecules per seven triplets in an asymmetric unit were found for the structures at 100 K and RT, respectively. These water molecules were classified into two groups, those in the first and second hydration shells. Although there was no significant difference between water molecules in the first shell at 100 K and those at RT, a significant difference between those in the second shell was observed. That is, the number of water molecules at RT decreased to one half and the average distance from peptide chains at RT became longer by about 0.3 A. On the other hand, of seven triplets in an asymmetric unit, three proline residues at the X position at 100 K clearly showed an up-puckering conformation, as opposed to the recent propensity-based hypothesis for the stabilization and destabilization of triple-helical structures by proline hydroxylation. This puckering was attributed to the interaction between proline rings and the surrounding water molecules at 100 K, which is much weaker at RT, as shown by longer average distance from peptide chains.


  • Organizational Affiliation

    Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan. okuyamak@cc.tuat.ac.jp


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
collagen like peptide7N/AMutation(s): 0 
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
collagen like peptide7N/AMutation(s): 0 
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
collagen like peptide7N/AMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
A
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.133 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 13.864α = 90
b = 26.181β = 105.75
c = 19.877γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
SHELXmodel building
SHELXL-97refinement
CrystalCleardata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-03
    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: 2013-12-25
    Changes: Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Refinement description