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- PDB-4l40: Structure of the P450 OleT with a C20 fatty acid substrate bound -

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Basic information

Entry
Database: PDB / ID: 4l40
TitleStructure of the P450 OleT with a C20 fatty acid substrate bound
ComponentsTerminal olefin-forming fatty acid decarboxylase
KeywordsOXIDOREDUCTASE / cytochrome P450 / peroxygenase / fatty acid decarboxylase
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLeys, D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure and Biochemical Properties of the Alkene Producing Cytochrome P450 OleTJE (CYP152L1) from the Jeotgalicoccus sp. 8456 Bacterium.
Authors: Belcher, J. / McLean, K.J. / Matthews, S. / Woodward, L.S. / Fisher, K. / Rigby, S.E. / Nelson, D.R. / Potts, D. / Baynham, M.T. / Parker, D.A. / Leys, D. / Munro, A.W.
History
DepositionJun 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,3583
Polymers48,4291
Non-polymers9292
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.630, 59.630, 244.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Terminal olefin-forming fatty acid decarboxylase


Mass: 48428.906 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-DCR / icosanoic acid


Mass: 312.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H40O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride 0.1 M Tris, 10% w/v PEG 8K, 10% w/v PEG 1K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→33.6 Å / Num. all: 15317 / Num. obs: 15317 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1IZO

1izo


Resolution: 2.5→33.6 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.873 / SU B: 9.513 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.968 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26914 811 5 %RANDOM
Rwork0.19523 ---
obs0.19878 15317 100 %-
all-15317 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.339 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 65 145 3592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223533
X-RAY DIFFRACTIONr_bond_other_d0.0010.022449
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9944791
X-RAY DIFFRACTIONr_angle_other_deg0.90435923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84923.663172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14215599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3131528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02736
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_it0.6021.52083
X-RAY DIFFRACTIONr_mcbond_other0.1181.5849
X-RAY DIFFRACTIONr_mcangle_it1.18423375
X-RAY DIFFRACTIONr_scbond_it2.02731450
X-RAY DIFFRACTIONr_scangle_it3.3284.51416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 62 -
Rwork0.279 1097 -
obs--100 %

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