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- PDB-5m0p: Crystal structure of cytochrome P450 OleT F79A in complex with ar... -

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Basic information

Entry
Database: PDB / ID: 5m0p
TitleCrystal structure of cytochrome P450 OleT F79A in complex with arachidonic acid
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
icosanoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesJeotgalicoccus sp. ATCC 8456 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsTee, K.L. / Munro, A. / Matthews, S. / Leys, D. / Levy, C.
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 1.1Dec 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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,2447
Polymers98,3632
Non-polymers1,8815
Water12,629701
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A: Terminal olefin-forming fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1113
Polymers49,1821
Non-polymers9292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Terminal olefin-forming fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1344
Polymers49,1821
Non-polymers9523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.880, 110.120, 164.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Terminal olefin-forming fatty acid decarboxylase


Mass: 49181.684 Da / Num. of mol.: 2 / Mutation: F79A
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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DCR / icosanoic acid


Mass: 312.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H40O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 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: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→55.12 Å / Num. obs: 66360 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
xia2data scaling
RefinementResolution: 1.95→55.12 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.406 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 3443 4.9 %RANDOM
Rwork0.15718 ---
obs0.15937 66360 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.706 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å2-0 Å2
2---1.97 Å2-0 Å2
3----1.51 Å2
Refinement stepCycle: 1 / Resolution: 1.95→55.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6792 0 131 701 7624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197182
X-RAY DIFFRACTIONr_bond_other_d0.0010.026787
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9729753
X-RAY DIFFRACTIONr_angle_other_deg1.15315596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3775861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87223.668349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.449151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.871558
X-RAY DIFFRACTIONr_chiral_restr0.0890.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218179
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021717
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_restr5.894313967
X-RAY DIFFRACTIONr_sphericity_free11.695261
X-RAY DIFFRACTIONr_sphericity_bonded4.995514228
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 257 -
Rwork0.271 4861 -
obs--99.9 %

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