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- PDB-5m0n: Crystal structure of cytochrome P450 OleT in complex with formate -

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Basic information

Entry
Database: PDB / ID: 5m0n
TitleCrystal structure of cytochrome P450 OleT in complex with formate
ComponentsTerminal olefin-forming fatty acid decarboxylase
KeywordsOXIDOREDUCTASE / cytochrome P450 / decarboxylase / oxidase / peroxide
Function / homology
Function and homology information


sterol metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesJeotgalicoccus sp. ATCC 8456 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.44 Å
AuthorsTee, K.L. / Munro, A. / Matthews, S. / Leys, D. / Levy, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K017802/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N006275/1 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Catalytic Determinants of Alkene Production by the Cytochrome P450 Peroxygenase OleTJE.
Authors: Matthews, S. / Belcher, J.D. / Tee, K.L. / Girvan, H.M. / McLean, K.J. / Rigby, S.E. / Levy, C.W. / Leys, D. / Parker, D.A. / Blankley, R.T. / Munro, A.W.
History
DepositionOct 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terminal olefin-forming fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0164
Polymers49,2581
Non-polymers7593
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-28 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.170, 60.170, 241.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-502-

SO4

21A-858-

HOH

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Components

#1: Protein Terminal olefin-forming fatty acid decarboxylase


Mass: 49257.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jeotgalicoccus sp. ATCC 8456 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: E9NSU2
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Diffracting crystals were grown in 0.2 M MgCl2, 0.1 M HEPES, 20% PEG 6000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.44→48.21 Å / Num. obs: 77736 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 25.8
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4L40

4l40


Resolution: 1.44→48.21 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.838 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.056 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17262 3948 4.8 %RANDOM
Rwork0.13455 ---
obs0.13639 77736 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.44→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 51 321 3790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193564
X-RAY DIFFRACTIONr_bond_other_d0.0020.023347
X-RAY DIFFRACTIONr_angle_refined_deg2.021.9694839
X-RAY DIFFRACTIONr_angle_other_deg1.07237688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29223.714175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90215610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0561528
X-RAY DIFFRACTIONr_chiral_restr0.1330.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214041
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02853
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.33236907
X-RAY DIFFRACTIONr_sphericity_free19.5065116
X-RAY DIFFRACTIONr_sphericity_bonded14.28557029
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 286 -
Rwork0.214 5628 -
obs--100 %

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