3KLR

Bovine H-protein at 0.88 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.112 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution

Higashiura, A.Kurakane, T.Matsuda, M.Suzuki, M.Inaka, K.Sato, M.Kobayashi, T.Tanaka, T.Tanaka, H.Fujiwara, K.Nakagawa, A.

(2010) Acta Crystallogr D Biol Crystallogr 66: 698-708

  • DOI: https://doi.org/10.1107/S0907444910010668
  • Primary Citation of Related Structures:  
    3KLR

  • PubMed Abstract: 

    Recent technical improvements in macromolecular X-ray crystallography have significantly improved the resolution limit of protein structures. However, examples of high-resolution structure determination are still limited. In this study, the X-ray crystal structure of bovine H-protein, a component of the glycine cleavage system, was determined at 0.88 A resolution. This is the first ultrahigh-resolution structure of an H-protein. The data were collected using synchrotron radiation. Because of limitations of the hardware, especially the dynamic range of the CCD detector, three data sets (high-, medium- and low-resolution data sets) were measured in order to obtain a complete set of data. To improve the quality of the merged data, the reference data set was optimized for merging and the merged data were assessed by comparing merging statistics and R factors against the final model and the number of visualized H atoms. In addition, the advantages of merging three data sets were evaluated. The omission of low-resolution reflections had an adverse effect on visualization of H atoms in hydrogen-omit maps. Visualization of hydrogen electron density is a good indicator for assessing the quality of high-resolution X-ray diffraction data.


  • Organizational Affiliation

    Institute for Protein Research, Osaka University, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine cleavage system H protein125Bos taurusMutation(s): 0 
UniProt
Find proteins for P20821 (Bos taurus)
Explore P20821 
Go to UniProtKB:  P20821
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20821
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.112 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.584α = 90
b = 41.295β = 91.18
c = 43.124γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-11-01
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description