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- PDB-7q89: OleP mutant G92W in complex with 6DEB -

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Basic information

Entry
Database: PDB / ID: 7q89
TitleOleP mutant G92W in complex with 6DEB
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Oleandomicine / OleP / mutant / 6DEB
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 / FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSavino, C. / Montemiglio, L.C. / Vallone, B. / Exertier, C. / Freda, I. / Gugole, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2021
Title: Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics.
Authors: Montemiglio, L.C. / Gugole, E. / Freda, I. / Exertier, C. / D'Auria, L. / Chen, C.G. / Nardi, A.N. / Cerutti, G. / Parisi, G. / D'Abramo, M. / Savino, C. / Vallone, B.
History
DepositionNov 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)285,105174
Polymers271,6766
Non-polymers13,428168
Water24,1221339
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,40046
Polymers45,2791
Non-polymers3,12045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,21544
Polymers45,2791
Non-polymers2,93643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,77834
Polymers45,2791
Non-polymers2,49933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,04220
Polymers45,2791
Non-polymers1,76219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,90416
Polymers45,2791
Non-polymers1,62415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,76614
Polymers45,2791
Non-polymers1,48613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.758, 110.489, 159.818
Angle α, β, γ (deg.)90.00, 129.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-855-

HOH

21D-753-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Cytochrome P-450


Mass: 45279.375 Da / Num. of mol.: 6 / Mutation: G92W
Source method: isolated from a genetically manipulated source
Details: Cytochrome P450 OleP mutant G92W / Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59819

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Non-polymers , 6 types, 1507 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-DEB / 6-DEOXYERYTHRONOLIDE B


Mass: 386.523 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H38O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 139 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1339 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium Formate 4.4M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2019
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→48.1 Å / Num. obs: 462764 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.34
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 3 % / Num. unique obs: 227594 / CC1/2: 0.323 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mns

5mns


Resolution: 2.08→48.03 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.565 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22779 9963 5 %RANDOM
Rwork0.17037 ---
obs0.17331 188451 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0.06 Å2
2--0.15 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.08→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18686 0 899 1339 20924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01320977
X-RAY DIFFRACTIONr_bond_other_d0.0020.01719944
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.67528581
X-RAY DIFFRACTIONr_angle_other_deg1.361.59145868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82752652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.07219.9511216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93153358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.20215246
X-RAY DIFFRACTIONr_chiral_restr0.0890.22688
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0223925
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025011
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_it5.4965.5639883
X-RAY DIFFRACTIONr_mcbond_other5.4965.5639884
X-RAY DIFFRACTIONr_mcangle_it7.1648.32812422
X-RAY DIFFRACTIONr_mcangle_other7.1648.32912423
X-RAY DIFFRACTIONr_scbond_it6.1286.05911094
X-RAY DIFFRACTIONr_scbond_other6.1286.05911095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1718.82916032
X-RAY DIFFRACTIONr_long_range_B_refined10.86266.43823593
X-RAY DIFFRACTIONr_long_range_B_other10.86266.43923594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 718 -
Rwork0.353 13945 -
obs--99.94 %

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