3KZA | pdb_00003kza

Crystal structure of Gyuba, a patched chimera of b-lactglobulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.285 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Structure and stability of Gyuba, a patched chimera of b-lactoglobulin

Ohtomo, H.Konuma, T.Utsunoiya, H.Tsuge, H.Ikeguchi, M.

(2011) Protein Sci 20: 1867-1875

  • DOI: https://doi.org/10.1002/pro.720
  • Primary Citation Related Structures: 
    3KZA

  • PubMed Abstract: 

    β-lactoglobulin (LG) contains nine β-strands (strands A-I) and one α-helix. Strands A-H form a β-barrel. At neutral pH, equine LG (ELG) is monomeric, whereas bovine LG (BLG) is dimeric, and the I-strands of its two subunits form an intermolecular β-sheet. We previously constructed a chimeric ELG in which the sequence of the I-strand was replaced with that of BLG. This chimera did not dimerize. For this study, we constructed the new chimera we call Gyuba (which means cow and horse in Japanese). The amino acid sequence of Gyuba includes the sequences of the BLG secondary structures and those of the ELG loops. The crystal structure of Gyuba is very similar to that of BLG and indicates that Gyuba dimerizes via the intermolecular β-sheet formed by the two I-strands. Thus, the entire arrangement of the secondary structural elements is important for LG dimer formation.


  • Organizational Affiliation
    • Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan.

Macromolecule Content 

  • Total Structure Weight: 36.62 kDa 
  • Atom Count: 2,576 
  • Modeled Residue Count: 298 
  • Deposited Residue Count: 324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactoglobulin
A, B
162Equus caballusBos taurusMutation(s): 2 
Gene Names: LGB1
UniProt
Find proteins for P02754 (Bos taurus)
Explore P02754 
Go to UniProtKB:  P02754
Find proteins for P02758 (Equus caballus)
Explore P02758 
Go to UniProtKB:  P02758
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP02758P02754
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.285 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.925α = 90
b = 68.925β = 90
c = 151.616γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-09
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2021-11-10
    Changes: Database references
  • Version 1.5: 2024-11-13
    Changes: Data collection, Structure summary