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- PDB-7q6x: OleP mutant S240Y in complex with 6DEB -

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Basic information

Entry
Database: PDB / ID: 7q6x
TitleOleP mutant S240Y 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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
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: 2.7 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 1.2Apr 6, 2022Group: Advisory / Derived calculations / Structure summary
Category: entity_name_com / pdbx_validate_close_contact ...entity_name_com / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3Jan 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

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)275,59224
Polymers269,2986
Non-polymers6,29418
Water4,035224
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0246
Polymers44,8831
Non-polymers1,1415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8863
Polymers44,8831
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9324
Polymers44,8831
Non-polymers1,0493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9324
Polymers44,8831
Non-polymers1,0493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9324
Polymers44,8831
Non-polymers1,0493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8863
Polymers44,8831
Non-polymers1,0032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)248.624, 110.355, 160.046
Angle α, β, γ (deg.)90.00, 129.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cytochrome P-450


Mass: 44882.938 Da / Num. of mol.: 6 / Mutation: S240Y
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.: 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
#4: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: Sodium Formate, 4.4 M

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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 12, 2020
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: 2.5→51.34 Å / Num. obs: 225386 / % possible obs: 99.2 % / Redundancy: 4 % / CC1/2: 0.992 / Net I/σ(I): 5.59
Reflection shellResolution: 2.5→2.65 Å / Num. unique obs: 36239 / CC1/2: 0.1 / % possible all: 99.1

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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: 2.7→51.34 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 19.676 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 1.233 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26804 4388 4.8 %RANDOM
Rwork0.20414 ---
obs0.20721 87164 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.582 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å2-0.23 Å2
2--1.84 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.7→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18627 0 438 224 19289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01321198
X-RAY DIFFRACTIONr_bond_other_d0.0020.01720225
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.67629269
X-RAY DIFFRACTIONr_angle_other_deg1.2351.58846696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80752793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31720.1661325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.137153526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.38815261
X-RAY DIFFRACTIONr_chiral_restr0.0680.22750
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224475
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025047
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_it3.3486.86810030
X-RAY DIFFRACTIONr_mcbond_other3.3486.86810031
X-RAY DIFFRACTIONr_mcangle_it5.42510.31512643
X-RAY DIFFRACTIONr_mcangle_other5.42410.31612644
X-RAY DIFFRACTIONr_scbond_it3.0287.1311168
X-RAY DIFFRACTIONr_scbond_other3.0267.12811163
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.03610.59116407
X-RAY DIFFRACTIONr_long_range_B_refined7.74177.08322516
X-RAY DIFFRACTIONr_long_range_B_other7.7477.08222513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.518 386 -
Rwork0.489 6347 -
obs--99.97 %

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