1HBZ

Catalase from Micrococcus lysodeikticu


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.120 (Depositor), 0.130 (DCC) 
  • R-Value Work: 
    0.092 (Depositor), 0.110 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Three-Dimensional Structure of Catalase from Micrococcus Lysodeikticus at 1.5A Resolution

Murshudov, G.N.Melik-Adamyan, W.R.Grebenko, A.I.Barynin, V.V.Vagin, A.A.Vainshtein, B.K.Dauter, Z.Wilson, K.S.

(1992) FEBS Lett 312: 127

  • DOI: https://doi.org/10.1016/0014-5793(92)80919-8
  • Primary Citation of Related Structures:  
    1HBZ

  • PubMed Abstract: 

    The three-dimensional crystal structure of catalase from Micrococcus lysodeikticus has been solved by multiple isomorphous replacement and refined at 1.5 A resolution. The subunit of the tetrameric molecule of 222 symmetry consists of a single polypeptide chain of about 500 amino acid residues and one haem group. The crystals belong to space group P4(2)2(1)2 with unit cell parameters a = b = 106.7 A, c = 106.3 A, and there is one subunit of the tetramer per asymmetric unit. The amino acid sequence has been tentatively determined by computer graphics model building and comparison with the known three-dimensional structure of beef liver catalase and sequences of several other catalases. The atomic model has been refined by Hendrickson and Konnert's least-squares minimisation against 94,315 reflections between 8 A and 1.5 A. The final model consists of 3,977 non-hydrogen atoms of the protein and haem group, 426 water molecules and one sulphate ion. The secondary and tertiary structures of the bacterial catalase have been analyzed and a comparison with the structure of beef liver catalase has been made.


  • Organizational Affiliation

    Institute of Crystallography, Russian Academy of Sciences, Moscow.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATALASE498Micrococcus luteusMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for P29422 (Micrococcus luteus)
Explore P29422 
Go to UniProtKB:  P29422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29422
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.120 (Depositor), 0.130 (DCC) 
  • R-Value Work:  0.092 (Depositor), 0.110 (DCC) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.7α = 90
b = 106.7β = 90
c = 106.25γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-24
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other