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- PDB-8qrd: OleP in complex with testosterone in high salt crystallization co... -

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Basic information

Entry
Database: PDB / ID: 8qrd
TitleOleP in complex with testosterone in high salt crystallization conditions
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / testosterone / complex
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 / TESTOSTERONE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFata, F. / Costanzo, A. / Freda, I. / Gugole, E. / Bulfaro, G. / Barbizzi, L. / Di Renzo, M. / Savino, C. / Vallone, B. / Montemiglio, L.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP.
Authors: Costanzo, A. / Fata, F. / Freda, I. / De Sciscio, M.L. / Gugole, E. / Bulfaro, G. / Di Renzo, M. / Barbizzi, L. / Exertier, C. / Parisi, G. / D'Abramo, M. / Vallone, B. / Savino, C. / Montemiglio, L.C.
History
DepositionOct 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)279,45170
Polymers271,7666
Non-polymers7,68564
Water13,187732
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,49810
Polymers45,2941
Non-polymers1,2049
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,82117
Polymers45,2941
Non-polymers1,52616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,77516
Polymers45,2941
Non-polymers1,48015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,54411
Polymers45,2941
Non-polymers1,25010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3607
Polymers45,2941
Non-polymers1,0666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4529
Polymers45,2941
Non-polymers1,1588
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)248.195, 109.738, 160.130
Angle α, β, γ (deg.)90.00, 129.41, 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: 45294.348 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 , 5 types, 796 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-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 60.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 4.4 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.0002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0002 Å / Relative weight: 1
ReflectionResolution: 2.3→66.07 Å / Num. obs: 147079 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.785 / Num. unique obs: 7268 / CC1/2: 0.509

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.75 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.956 / SU B: 14.695 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21226 7266 4.9 %RANDOM
Rwork0.1653 ---
obs0.16762 139800 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.647 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0 Å20 Å2
2--0.76 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.3→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18919 0 144 732 19795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01220019
X-RAY DIFFRACTIONr_bond_other_d0.0010.01618944
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.86427434
X-RAY DIFFRACTIONr_angle_other_deg0.561.76443568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43552527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.0555232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.275103192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.23097
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224290
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024646
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_it2.5223.4589739
X-RAY DIFFRACTIONr_mcbond_other2.5223.4599740
X-RAY DIFFRACTIONr_mcangle_it3.8096.21712230
X-RAY DIFFRACTIONr_mcangle_other3.8096.21712231
X-RAY DIFFRACTIONr_scbond_it3.4753.87510280
X-RAY DIFFRACTIONr_scbond_other3.3523.84210189
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2866.91215150
X-RAY DIFFRACTIONr_long_range_B_refined7.61235.3722019
X-RAY DIFFRACTIONr_long_range_B_other7.61535.2721934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 512 -
Rwork0.283 10277 -
obs--99.96 %
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)
12.02430.06620.33472.13941.15751.87290.0876-0.16970.06360.092-0.0513-0.1908-0.07060.0227-0.03630.05530.0460.00880.14760.02760.068669.1046-79.277-19.446
23.3373-0.1787-0.770.86410.4051.73540.04740.1436-0.10460.0078-0.05930.1295-0.0221-0.17020.01190.04110.0468-0.04740.0671-0.05950.0819-43.0852-50.2054-62.3391
31.3527-0.0526-0.03210.98140.67021.7880.01850.1082-0.0427-0.0477-0.0069-0.0675-0.0974-0.0343-0.01160.01990.01580.01310.023-0.00460.0738-3.4282-77.2006-81.9247
42.8821-0.7154-0.35091.08060.55971.97870.0910.1168-0.1667-0.0930.00670.08470.08270.0041-0.09770.09010.0664-0.10330.21-0.17690.184630.7233-49.4635-1.2746
51.2708-0.04050.34973.19010.68252.039-0.00140.07730.084-0.0880.1329-0.1229-0.06740.2354-0.13150.11790.0526-0.05790.23630.0090.211621.7587-40.2157-41.0866
61.22920.56410.75552.45780.16691.4361-0.14950.5432-0.0956-0.44120.2204-0.27490.0240.3601-0.07090.2597-0.0733-0.01560.4229-0.0490.2542-50.6811-33.5595-102.6993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 601
2X-RAY DIFFRACTION2B11 - 601
3X-RAY DIFFRACTION3C12 - 601
4X-RAY DIFFRACTION4D11 - 601
5X-RAY DIFFRACTION5E13 - 601
6X-RAY DIFFRACTION6F11 - 601

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