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- PDB-8qyi: OleP in complex with lithocholic acid in high salt crystallizatio... -

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Basic information

Entry
Database: PDB / ID: 8qyi
TitleOleP in complex with lithocholic acid in high salt crystallization conditions
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / lithocholic acid / 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 / 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 26, 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)275,205126
Polymers264,4146
Non-polymers10,791120
Water13,457747
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,09826
Polymers44,0691
Non-polymers2,02925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,09826
Polymers44,0691
Non-polymers2,02925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,19028
Polymers44,0691
Non-polymers2,12127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,68317
Polymers44,0691
Non-polymers1,61416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,54514
Polymers44,0691
Non-polymers1,47613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59115
Polymers44,0691
Non-polymers1,52214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)249.373, 109.269, 160.658
Angle α, β, γ (deg.)90.00, 129.60, 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: 44069.059 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, 867 molecules

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


Mass: 616.487 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-4OA / (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid / Lithocholic acid


Mass: 376.573 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: CH2O2
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 747 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→80.33 Å / Num. obs: 147134 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.363 / Num. unique obs: 7277 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→80.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 13.736 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22167 7213 4.9 %RANDOM
Rwork0.17322 ---
obs0.17555 139909 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.496 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0 Å2-0.51 Å2
2--1.55 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.3→80.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18520 0 732 747 19999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01319811
X-RAY DIFFRACTIONr_bond_other_d0.0010.01418764
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.67126973
X-RAY DIFFRACTIONr_angle_other_deg1.351.58943080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13252427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.62920.1871121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.487153110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.80515218
X-RAY DIFFRACTIONr_chiral_restr0.0880.22525
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222452
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024632
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_it1.9473.3019564
X-RAY DIFFRACTIONr_mcbond_other1.9473.3029565
X-RAY DIFFRACTIONr_mcangle_it2.9834.94911961
X-RAY DIFFRACTIONr_mcangle_other2.9834.94911962
X-RAY DIFFRACTIONr_scbond_it2.7833.69710247
X-RAY DIFFRACTIONr_scbond_other2.4763.62510042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8785.36814987
X-RAY DIFFRACTIONr_long_range_B_refined6.35439.84621435
X-RAY DIFFRACTIONr_long_range_B_other6.35439.84321435
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
Rfree0.311 553 -
Rwork0.274 10277 -
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)
11.8754-0.12570.62521.7217-1.0712.23440.0239-0.02390.07570.0591-0.02510.0829-0.24990.00030.00110.0517-0.0320.00880.0723-0.01990.0217-69.4567-23.828219.4239
23.2970.1687-0.69670.8048-0.32941.85750.0084-0.083-0.0917-0.0257-0.0203-0.11550.00850.15580.0120.0511-0.0458-0.04750.05590.04730.070943.35694.464262.1128
31.2363-0.04650.06991.2479-0.72771.8378-0.0045-0.0874-0.04390.05540.01830.0902-0.1132-0.0316-0.01380.0233-0.0166-0.00260.02890.01470.05333.2636-22.172981.9681
42.54470.446-0.39840.8322-0.45421.76810.0659-0.148-0.16090.0377-0.0411-0.08640.12280.0446-0.02480.1301-0.0726-0.11410.12260.12690.1511-30.75075.35831.117
51.36660.28590.45312.945-0.82682.0171-0.0369-0.11720.08650.02510.1210.2226-0.1043-0.2424-0.08410.1266-0.0382-0.04690.2297-0.0010.1969-21.893614.35341.0481
61.2874-0.59720.52382.3972-0.451.5544-0.1054-0.4673-0.11750.41610.15870.2227-0.0238-0.2324-0.05330.21210.014-0.02390.34930.00780.192450.841320.8182102.8191
700000000000000-00.1945000.194500.1945000
800000000000000-00.1945000.194500.1945000
900000000000000-00.1945000.194500.1945000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 407
2X-RAY DIFFRACTION2B12 - 407
3X-RAY DIFFRACTION3C10 - 407
4X-RAY DIFFRACTION4D11 - 407
5X-RAY DIFFRACTION5E14 - 407
6X-RAY DIFFRACTION6F12 - 407

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