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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1107/S0907444910010668
  • Structures With Same Primary Citation

  • 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 cry ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycine cleavage system H proteinA125Bos taurusMutation(s): 0 
Gene Names: GCSH
Find proteins for P20821 (Bos taurus)
Explore P20821 
Go to UniProtKB:  P20821
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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

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Entry History 

Deposition Data

Revision History 

  • 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