2DBY

Crystal structure of the GTP-binding protein YchF in complexed with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.221 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the GTP-binding protein YchF in complexed with GDP

Kukimoto-Niino, M.Murayama, K.Shirouzu, M.Kuramitsu, S.Yokoyama, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein368Thermus thermophilus HB8Mutation(s): 2 
UniProt
Find proteins for Q5SJ29 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJ29 
Go to UniProtKB:  Q5SJ29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJ29
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.384α = 90
b = 133.169β = 90
c = 46.432γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary