3WN8

Crystal Structure of Collagen-Model Peptide, (POG)3-PRG-(POG)4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report



Literature

Preferred side-chain conformation of arginine residues in a triple-helical structure.

Okuyama, K.Haga, M.Noguchi, K.Tanaka, T.

(2014) Biopolymers 101: 1000-1009

  • DOI: 10.1002/bip.22478
  • Primary Citation of Related Structures:  
    3WN8

  • PubMed Abstract: 
  • The crystal structure of the triple-helical peptide (Pro-Hyp-Gly)3 -Pro-Arg-Gly-(Pro-Hyp-Gly)4 (POG3-PRG-POG4) was determined at 1.45 Å resolution. POG3-PRG-POG4 was designed to permit investigation of the side-chain conformation of the Arg residues ...

    The crystal structure of the triple-helical peptide (Pro-Hyp-Gly)3 -Pro-Arg-Gly-(Pro-Hyp-Gly)4 (POG3-PRG-POG4) was determined at 1.45 Å resolution. POG3-PRG-POG4 was designed to permit investigation of the side-chain conformation of the Arg residues in a triple-helical structure. Because of the alternative structure of one of three Arg residues, four side-chain conformations were observed in an asymmetric unit. Among them, three adopt a ttg(-) t conformation and the other adopts a tg(-) g(-) t conformation. A statistical analysis of 80 Arg residues in various triple-helical peptides showed that, unlike those in globular proteins, they preferentially adopt a tt conformation for χ1 and χ2 , as observed in POG3-PRG-POG4. This conformation permits van der Waals contacts between the side-chain atoms of Arg and the main-chain atoms of the adjacent strand in the same molecule. Unlike many other host-guest peptides, in which there is a significant difference between the helical twists in the guest and the host peptides, POG3-PRG-POG4 shows a marked difference between the helical twists in the N-terminal peptide and those in the C-terminal peptide, separated near the Arg residue. This suggested that the unique side-chain conformation of the Arg residue affects not only the conformation of the guest peptide, but also the conformation of the peptide away from the Arg residue.


    Organizational Affiliation

    Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
collagen-like peptideABC24N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A,B,CL-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.285α = 90
b = 19.567β = 94.51
c = 49.022γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
X-PLORmodel building
SHELXL-97refinement
CrystalCleardata reduction
CrystalCleardata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release