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- PDB-7q6r: OleP mutant E89Y in complex with 6DEB -

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Basic information

Entry
Database: PDB / ID: 7q6r
TitleOleP mutant E89Y in complex with 6DEB
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Oleandomicine / OleP / mutant / 6DEB
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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: 2.44 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 9, 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)273,44565
Polymers264,6196
Non-polymers8,82659
Water6,756375
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,61212
Polymers44,1031
Non-polymers1,50911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,75114
Polymers44,1031
Non-polymers1,64713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,84316
Polymers44,1031
Non-polymers1,74015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52010
Polymers44,1031
Non-polymers1,4179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3366
Polymers44,1031
Non-polymers1,2335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3827
Polymers44,1031
Non-polymers1,2796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)248.135, 111.117, 160.543
Angle α, β, γ (deg.)90.00, 129.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-641-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Cytochrome P-450


Mass: 44103.121 Da / Num. of mol.: 6 / Mutation: E89Y
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 , 5 types, 434 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 294 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: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.44→48.07 Å / Num. obs: 241832 / % possible obs: 98.2 % / Redundancy: 3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.55
Reflection shellResolution: 2.44→2.59 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 109337 / CC1/2: 0.747 / % possible all: 96.7

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Processing

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

5mns


Resolution: 2.44→48.07 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.507 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24333 5991 4.9 %RANDOM
Rwork0.18714 ---
obs0.18988 117365 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.212 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å2-0 Å2-1.11 Å2
2--2.45 Å20 Å2
3---0.93 Å2
Refinement stepCycle: 1 / Resolution: 2.44→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18485 0 603 375 19463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01320524
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719607
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.67628123
X-RAY DIFFRACTIONr_angle_other_deg1.2131.58845098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79452603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.99919.8631238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.249153344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.54615253
X-RAY DIFFRACTIONr_chiral_restr0.070.22624
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223424
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024890
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_it4.6056.1889778
X-RAY DIFFRACTIONr_mcbond_other4.6046.1889779
X-RAY DIFFRACTIONr_mcangle_it6.6769.28712292
X-RAY DIFFRACTIONr_mcangle_other6.6759.28812293
X-RAY DIFFRACTIONr_scbond_it4.6226.60810746
X-RAY DIFFRACTIONr_scbond_other4.5986.59910681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8669.73115719
X-RAY DIFFRACTIONr_long_range_B_refined9.12970.30421783
X-RAY DIFFRACTIONr_long_range_B_other9.12970.30621784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.442→2.505 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 446 -
Rwork0.291 8461 -
obs--97.21 %

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