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Basic information

Entry
Database: PDB / ID: 5mns
TitleStructural and functional characterization of OleP in complex with 6DEB in sodium formate
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / P450 / cytochrome / 6DEB / epoxidase
Function / homology
Function and homology information


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, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
6-DEOXYERYTHRONOLIDE B / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsParisi, G. / Savino, C. / Montemiglio, L.C. / Vallone, B.
Funding support Italy, 1items
OrganizationGrant numberCountry
Istituto Pasteur Fondazione Cenci-BolognettiProt56/2013 Italy
CitationJournal: FASEB J. / Year: 2019
Title: Substrate-induced conformational change in cytochrome P450 OleP.
Authors: Parisi, G. / Montemiglio, L.C. / Giuffre, A. / Macone, A. / Scaglione, A. / Cerutti, G. / Exertier, C. / Savino, C. / Vallone, B.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P-450
B: Cytochrome P-450
C: Cytochrome P-450
D: Cytochrome P-450
E: Cytochrome P-450
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,09018
Polymers270,0726
Non-polymers6,01812
Water10,178565
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0153
Polymers45,0121
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0153
Polymers45,0121
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0153
Polymers45,0121
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0153
Polymers45,0121
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0153
Polymers45,0121
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0153
Polymers45,0121
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)247.600, 110.800, 159.100
Angle α, β, γ (deg.)90.00, 129.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cytochrome P-450


Mass: 45012.070 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59819
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-DEB / 6-DEOXYERYTHRONOLIDE B


Mass: 386.523 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H38O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4M HCOONa

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.62→120 Å / Num. obs: 98805 / % possible obs: 99.5 % / Redundancy: 6.09 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.63
Reflection shellResolution: 2.62→2.78 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XE3

4xe3


Resolution: 2.62→120 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.925 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 4932 5 %RANDOM
Rwork0.208 ---
obs0.211 93879 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.81 Å2
Baniso -1Baniso -2Baniso -3
1--3.13 Å20 Å2-0.85 Å2
2--2.04 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.62→120 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18447 0 420 565 19432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01919100
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218326
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.99626135
X-RAY DIFFRACTIONr_angle_other_deg0.995341960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67252371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81822.589846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.049152920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.55515202
X-RAY DIFFRACTIONr_chiral_restr0.0750.23015
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02121543
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024335
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_it2.4135.6329481
X-RAY DIFFRACTIONr_mcbond_other2.415.6329480
X-RAY DIFFRACTIONr_mcangle_it4.0028.44311844
X-RAY DIFFRACTIONr_mcangle_other4.0038.44411845
X-RAY DIFFRACTIONr_scbond_it2.1345.6689619
X-RAY DIFFRACTIONr_scbond_other2.1345.6689620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6728.44114289
X-RAY DIFFRACTIONr_long_range_B_refined6.51343.16421374
X-RAY DIFFRACTIONr_long_range_B_other6.48743.21121248
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 344 -
Rwork0.38 6641 -
obs--95.92 %

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