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- PDB-6zi7: Crystal structure of OleP-oleandolide(DEO) bound to L-rhamnose -

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Basic information

Entry
Database: PDB / ID: 6zi7
TitleCrystal structure of OleP-oleandolide(DEO) bound to L-rhamnose
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / cytochrome P450 / 8.8a-deoxyoleandolide monooxygenase / 8.8a-deoxyoleandolide / L-rhamnose
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 / alpha-L-rhamnopyranose / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 Å
AuthorsMontemiglio, L.C. / Savino, C. / Vallone, B. / Parisi, G. / Freda, I.
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 25, 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

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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)286,486241
Polymers270,0726
Non-polymers16,414235
Water24,4101355
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,41075
Polymers45,0121
Non-polymers4,39874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,84541
Polymers45,0121
Non-polymers2,83340
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,27953
Polymers45,0121
Non-polymers3,26752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,70738
Polymers45,0121
Non-polymers2,69537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,66818
Polymers45,0121
Non-polymers1,65617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,57616
Polymers45,0121
Non-polymers1,56415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.531, 110.683, 159.285
Angle α, β, γ (deg.)90.00, 129.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 9 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
#4: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1587 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
#5: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 214 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1355 / 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: 60.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4.4 M sodium formate (HCOONa)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.772 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.772 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 373419 / % possible obs: 99.1 % / Redundancy: 3.38 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.52
Reflection shellResolution: 2.11→2.24 Å / Rmerge(I) obs: 1.47 / Num. unique obs: 60223 / CC1/2: 0.484

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6ZHZ

6zhz


Resolution: 2.28→47.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.674 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24656 7488 5 %RANDOM
Rwork0.18384 ---
obs0.18697 143514 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.665 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å2-0.57 Å2
2--1.16 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.28→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18604 0 1095 1355 21054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01321465
X-RAY DIFFRACTIONr_bond_other_d0.0010.01720073
X-RAY DIFFRACTIONr_angle_refined_deg2.1641.68629279
X-RAY DIFFRACTIONr_angle_other_deg1.4381.60946443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31452768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12720.2211267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.266153465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.19215245
X-RAY DIFFRACTIONr_chiral_restr0.2190.22761
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0224830
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024937
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_it2.8054.1810009
X-RAY DIFFRACTIONr_mcbond_other2.8054.1810010
X-RAY DIFFRACTIONr_mcangle_it4.2436.2712610
X-RAY DIFFRACTIONr_mcangle_other4.2436.27112611
X-RAY DIFFRACTIONr_scbond_it3.1454.51711456
X-RAY DIFFRACTIONr_scbond_other2.9094.40211170
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4136.56116470
X-RAY DIFFRACTIONr_long_range_B_refined8.23549.15724013
X-RAY DIFFRACTIONr_long_range_B_other8.22749.11624004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 545 -
Rwork0.356 10577 -
obs--99.94 %
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)
10.95870.04250.17960.3519-0.35030.40630.14340.09730.07570.0633-0.08040.1052-0.02880.1191-0.0630.0407-0.0290.05510.1974-0.02280.1644-69.0417-24.310419.2972
20.8839-0.08670.07650.101-0.09410.23230.048-0.0737-0.1557-0.0072-0.0282-0.0613-0.0297-0.0079-0.01980.0294-0.0463-0.0080.20.09340.197642.84744.612262.1892
30.5289-0.0128-0.0870.0674-0.10940.21280.0267-0.0171-0.02530.0102-0.0161-0.0047-0.05110.0244-0.01060.0775-0.02550.02950.1768-0.00340.15623.5108-22.95781.3813
40.9699-0.060.04990.1908-0.2030.67550.2538-0.1175-0.21680.0324-0.0982-0.080.0193-0.0941-0.15560.0878-0.0957-0.11090.240.18370.2256-30.91315.431.5866
50.25440.19080.35310.95990.08360.7464-0.057-0.08540.053-0.11670.13920.1521-0.0233-0.0828-0.08220.0392-0.0248-0.05270.23370.04810.1921-21.927214.565141.0064
60.4926-0.33080.55841.1715-0.15670.6927-0.0784-0.2644-0.05810.05250.12390.0305-0.0852-0.2625-0.04550.01550.05890.00360.42450.12830.097950.644521.9432102.6079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 1201
2X-RAY DIFFRACTION2B8 - 701
3X-RAY DIFFRACTION3C8 - 628
4X-RAY DIFFRACTION4D8 - 611
5X-RAY DIFFRACTION5E11 - 603
6X-RAY DIFFRACTION6F10 - 604

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