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- PDB-6zhz: OleP-oleandolide(DEO) in high salt crystallization conditions -

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Basic information

Entry
Database: PDB / ID: 6zhz
TitleOleP-oleandolide(DEO) in high 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
FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Chem-QR8 / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMontemiglio, L.C. / Savino, 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 24, 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)281,689124
Polymers270,0726
Non-polymers11,617118
Water13,745763
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,88320
Polymers45,0121
Non-polymers1,87119
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,68134
Polymers45,0121
Non-polymers2,66933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,54331
Polymers45,0121
Non-polymers2,53130
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,60614
Polymers45,0121
Non-polymers1,59413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,36911
Polymers45,0121
Non-polymers1,35710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,60614
Polymers45,0121
Non-polymers1,59413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.469, 111.215, 159.203
Angle α, β, γ (deg.)90.00, 129.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 7 types, 881 molecules

#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-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.: 6 / Source method: obtained synthetically / Formula: C20H36O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 83 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 763 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4 M Sodium Formate (HCOONa)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→37.73 Å / Num. obs: 168218 / % possible obs: 98.9 % / Redundancy: 3.41 % / CC1/2: 0.99 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.33 Å / Rmerge(I) obs: 1.12 / Num. unique obs: 26579 / CC1/2: 0.51

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Processing

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

5mns


Resolution: 2.2→37.73 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / SU B: 20.089 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24313 8476 5 %RANDOM
Rwork0.18741 ---
obs0.19026 159658 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.09 Å2
2---0.67 Å20 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.2→37.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18491 0 782 763 20036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01319985
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718745
X-RAY DIFFRACTIONr_angle_refined_deg2.1631.68227208
X-RAY DIFFRACTIONr_angle_other_deg1.4651.60443187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.93352451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39320.2391131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.241153139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.97315219
X-RAY DIFFRACTIONr_chiral_restr0.2210.22546
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222664
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024441
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_it2.6844.3139654
X-RAY DIFFRACTIONr_mcbond_other2.6844.3149655
X-RAY DIFFRACTIONr_mcangle_it4.1786.46912105
X-RAY DIFFRACTIONr_mcangle_other4.1786.4712106
X-RAY DIFFRACTIONr_scbond_it3.2034.71910331
X-RAY DIFFRACTIONr_scbond_other3.2024.71910332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8226.87115088
X-RAY DIFFRACTIONr_long_range_B_refined7.97151.36522166
X-RAY DIFFRACTIONr_long_range_B_other7.97251.36722167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 566 -
Rwork0.413 11749 -
obs--98.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8917-0.14210.18460.6794-0.71230.80840.17390.16030.1690.0171-0.12740.1348-0.0080.1151-0.04660.0287-0.04520.02140.29390.00620.190554.91-0.889619.248
21.3157-0.2530.19980.662-0.21420.5450.00070.0242-0.07150.064-0.0094-0.12550.0197-0.0050.00870.0249-0.0521-0.05180.22240.07320.1636166.890228.521562.0372
30.7757-0.05010.00540.4055-0.24140.49260.0655-0.02870.01840.0156-0.0243-0.0059-0.04320.0094-0.04120.0179-0.0427-0.00390.1980.01510.1001127.57910.75781.2424
41.74410.171-0.37210.4768-0.23880.93340.1933-0.2202-0.1213-0.01680.0680.03690.0927-0.0962-0.26130.0686-0.1256-0.11540.41480.22720.230393.160929.41581.3386
51.06290.17870.71811.6393-0.09611.3094-0.0906-0.13760.1299-0.1140.21410.2558-0.0489-0.219-0.12350.0163-0.0069-0.03880.21360.04140.1674101.895538.140841.401
60.6236-0.23870.66841.3651-0.28811.5503-0.057-0.4104-0.00980.14030.10070.10440.0175-0.2684-0.04370.06180.0396-0.07570.44320.0340.1946174.357145.616102.3952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 501
2X-RAY DIFFRACTION2B11 - 450
3X-RAY DIFFRACTION3C12 - 450
4X-RAY DIFFRACTION4D13 - 501
5X-RAY DIFFRACTION5E13 - 450
6X-RAY DIFFRACTION6F13 - 501

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