4H23 | pdb_00004h23

Cytochrome P411BM3-CIS cyclopropanation catalyst


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.265 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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

This is version 1.4 of the entry. See complete history


Literature

A serine-substituted P450 catalyzes highly efficient carbene transfer to olefins in vivo.

Coelho, P.S.Wang, Z.J.Ener, M.E.Baril, S.A.Kannan, A.Arnold, F.H.Brustad, E.M.

(2013) Nat Chem Biol 9: 485-487

  • DOI: https://doi.org/10.1038/nchembio.1278
  • Primary Citation of Related Structures:  
    4H23, 4H24

  • PubMed Abstract: 

    Whole-cell catalysts for non-natural chemical reactions will open new routes to sustainable production of chemicals. We designed a cytochrome 'P411' with unique serine-heme ligation that catalyzes efficient and selective olefin cyclopropanation in intact Escherichia coli cells. The mutation C400S in cytochrome P450(BM3) gives a signature ferrous CO Soret peak at 411 nm, abolishes monooxygenation activity, raises the resting-state Fe(III)-to-Fe(II) reduction potential and substantially improves NAD(P)H-driven activity.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450-BM3 variant P411BM3-Cis
A, B
470Priestia megateriumMutation(s): 14 
Gene Names: CYP102A1cyp102
EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (UniProt)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19))
Explore P14779 
Go to UniProtKB:  P14779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14779
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.158α = 90
b = 124.455β = 90
c = 127.691γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report



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: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Database references
  • Version 1.3: 2013-12-18
    Changes: Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description