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- PDB-6zi2: OleP-oleandolide(DEO) in low salt crystallization conditions -

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Basic information

Entry
Database: PDB / ID: 6zi2
TitleOleP-oleandolide(DEO) in low salt crystallization conditions
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / cytochrome P450 / 8.8a-deoxyoleandolide monooxygenase / 8.8a-deoxyoleandolide
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-QR8 / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsSavino, C. / Montemiglio, L.C. / Vallone, B. / Parisi, G. / Cecchetti, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Pasteur Institute Italy
CitationJournal: Biomolecules / Year: 2020
Title: Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate.
Authors: Parisi, G. / Freda, I. / Exertier, C. / Cecchetti, C. / Gugole, E. / Cerutti, G. / D'Auria, L. / Macone, A. / Vallone, B. / Savino, C. / Montemiglio, L.C.
History
DepositionJun 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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
G: Cytochrome P-450
H: Cytochrome P-450
I: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,00927
Polymers405,1099
Non-polymers8,90118
Water1,72996
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0013
Polymers45,0121
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.066, 116.642, 125.170
Angle α, β, γ (deg.)104.43, 104.25, 113.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome P-450


Mass: 45012.070 Da / Num. of mol.: 9
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.: 9 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-QR8 / (3~{R},4~{S},5~{R},6~{S},7~{S},9~{S},11~{R},12~{S},13~{R},14~{R})-3,5,7,9,11,13,14-heptamethyl-4,6,12-tris(oxidanyl)-1-oxacyclotetradecane-2,10-dione


Mass: 372.496 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C20H36O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M NaCl 0.1 M Tris HCl pH 7.4 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8723 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8723 Å / Relative weight: 1
ReflectionResolution: 2.87→39.92 Å / Num. obs: 115590 / % possible obs: 98.2 % / Redundancy: 3.56 % / CC1/2: 0.99 / Rmerge(I) obs: 0.165 / Net I/σ(I): 7.29
Reflection shellResolution: 2.87→3.05 Å / Rmerge(I) obs: 0.924 / Num. unique obs: 18262 / CC1/2: 0.688

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MNV

5mnv


Resolution: 2.93→39.89 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.822 / SU B: 31.65 / SU ML: 0.524 / Cross valid method: THROUGHOUT / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29065 4684 5 %RANDOM
Rwork0.23894 ---
obs0.24153 88690 84.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.02 Å20.08 Å2
2---0.57 Å20.11 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.93→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26350 0 621 96 27067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01327594
X-RAY DIFFRACTIONr_bond_other_d0.0050.01726030
X-RAY DIFFRACTIONr_angle_refined_deg1.821.68437726
X-RAY DIFFRACTIONr_angle_other_deg1.4291.60159914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59753362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51520.1941549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.792154349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.89215299
X-RAY DIFFRACTIONr_chiral_restr0.10.23562
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0231061
X-RAY DIFFRACTIONr_gen_planes_other0.0050.026044
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_it4.7725.33713508
X-RAY DIFFRACTIONr_mcbond_other4.7725.33613507
X-RAY DIFFRACTIONr_mcangle_it7.6997.99316850
X-RAY DIFFRACTIONr_mcangle_other7.6997.99416851
X-RAY DIFFRACTIONr_scbond_it4.3855.49814086
X-RAY DIFFRACTIONr_scbond_other4.3855.49814086
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2288.16820877
X-RAY DIFFRACTIONr_long_range_B_refined11.20363.77831048
X-RAY DIFFRACTIONr_long_range_B_other11.20463.78531047
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.93→3.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 182 -
Rwork0.388 3602 -
obs--46.32 %

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