6GII | pdb_00006gii

The crystal structure of Tepidiphilus thermophilus P450 heme domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s.

Tavanti, M.Porter, J.L.Levy, C.W.Gomez Castellanos, J.R.Flitsch, S.L.Turner, N.J.

(2018) Biochem Biophys Res Commun 501: 846-850

  • DOI: https://doi.org/10.1016/j.bbrc.2018.05.014
  • Primary Citation of Related Structures:  
    6GII

  • PubMed Abstract: 

    The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes.


  • Organizational Affiliation

    Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450479Tepidiphilus thermophilusMutation(s): 0 
Gene Names: Ga0061068_103196
UniProt
Find proteins for A0A0K6ITW2 (Tepidiphilus thermophilus)
Explore A0A0K6ITW2 
Go to UniProtKB:  A0A0K6ITW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K6ITW2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.292α = 90
b = 74.384β = 90
c = 105.013γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

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 & Funding Information

Deposition Data

  • Released Date: 2018-05-30 
  • Deposition Author(s): Levy, C.W.

Funding OrganizationLocationGrant Number
European UnionUnited Kingdom613849
European UnionUnited Kingdom635734

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description