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- PDB-6wr0: Human steroidogenic cytochrome P450 17A1 with 3-keto-delta4-abira... -

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Basic information

Entry
Database: PDB / ID: 6wr0
TitleHuman steroidogenic cytochrome P450 17A1 with 3-keto-delta4-abiraterone analog
ComponentsSteroid 17-alpha-hydroxylase/17,20 lyase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / P450 / 17A1
Function / homology
Function and homology information


Defective CYP17A1 causes AH5 / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / glucocorticoid biosynthetic process / Androgen biosynthesis / hormone biosynthetic process / Glucocorticoid biosynthesis / androgen biosynthetic process / sex differentiation ...Defective CYP17A1 causes AH5 / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / glucocorticoid biosynthetic process / Androgen biosynthesis / hormone biosynthetic process / Glucocorticoid biosynthesis / androgen biosynthetic process / sex differentiation / progesterone metabolic process / steroid biosynthetic process / steroid metabolic process / oxygen binding / lyase activity / iron ion binding / axon / neuronal cell body / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-U7P / Steroid 17-alpha-hydroxylase/17,20 lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPetrunak, E.M. / Bart, A.G. / Scott, E.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102505 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Human cytochrome P450 17A1 structures with metabolites of prostate cancer drug abiraterone reveal substrate-binding plasticity and a second binding site.
Authors: Petrunak, E.M. / Bart, A.G. / Peng, H.M. / Auchus, R.J. / Scott, E.E.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: 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: Steroid 17-alpha-hydroxylase/17,20 lyase
B: Steroid 17-alpha-hydroxylase/17,20 lyase
C: Steroid 17-alpha-hydroxylase/17,20 lyase
D: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,92315
Polymers222,9614
Non-polymers3,96211
Water2,126118
1
A: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7043
Polymers55,7401
Non-polymers9642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7404
Polymers55,7401
Non-polymers9993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7404
Polymers55,7401
Non-polymers9993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7404
Polymers55,7401
Non-polymers9993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.347, 152.981, 168.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 31 through 503 or resid 600 through 601))A31 - 274
121(chain 'A' and (resid 31 through 503 or resid 600 through 601))A283 - 503
131(chain 'A' and (resid 31 through 503 or resid 600 through 601))A600 - 601
241chain 'B'B31 - 274
251chain 'B'B283 - 503
261chain 'B'B600 - 601
371(chain 'C' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))C31 - 274
381(chain 'C' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))C283 - 503
391(chain 'C' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))C600 - 601
4101(chain 'D' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))D31 - 274
4111(chain 'D' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))D283 - 503
4121(chain 'D' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))D600 - 601

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Components

#1: Protein
Steroid 17-alpha-hydroxylase/17,20 lyase / 17-alpha-hydroxyprogesterone aldolase / CYPXVII / Cytochrome P450 17A1 / Cytochrome P450-C17 / ...17-alpha-hydroxyprogesterone aldolase / CYPXVII / Cytochrome P450 17A1 / Cytochrome P450-C17 / Cytochrome P450c17 / Steroid 17-alpha-monooxygenase


Mass: 55740.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP17A1, CYP17, S17AH / Production host: Escherichia coli (E. coli)
References: UniProt: P05093, steroid 17alpha-monooxygenase, 17alpha-hydroxyprogesterone deacetylase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-U7P / (8alpha)-17-(pyridin-3-yl)androsta-4,16-dien-3-one / 3-keto-delta4-abiraterone analog


Mass: 347.493 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H29NO / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 175 mM Tris HCl, pH 8.5, 30% PEG-3350, 350 mM LiSO4, and 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→39.81 Å / Num. obs: 64672 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 53.1 Å2 / Rpim(I) all: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9236 / Rpim(I) all: 0.552 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SWZ

3swz


Resolution: 2.7→39.81 Å / SU ML: 0.3474 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.8513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 3264 5.06 %
Rwork0.209 61282 -
obs0.2109 64546 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.83 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14905 0 279 118 15302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016915547
X-RAY DIFFRACTIONf_angle_d1.390721132
X-RAY DIFFRACTIONf_chiral_restr0.0912369
X-RAY DIFFRACTIONf_plane_restr0.00832666
X-RAY DIFFRACTIONf_dihedral_angle_d20.21385776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.3611330.31732518X-RAY DIFFRACTION94.07
2.74-2.780.36821400.30522614X-RAY DIFFRACTION99.64
2.78-2.830.31161360.29482636X-RAY DIFFRACTION99.53
2.83-2.880.34591430.27962623X-RAY DIFFRACTION99.71
2.88-2.930.29661570.28542621X-RAY DIFFRACTION99.68
2.93-2.990.31571410.26862650X-RAY DIFFRACTION99.86
2.99-3.050.33621470.29212622X-RAY DIFFRACTION99.93
3.05-3.110.27451340.2742679X-RAY DIFFRACTION100
3.11-3.190.31221270.26592648X-RAY DIFFRACTION99.75
3.19-3.270.32331370.2472640X-RAY DIFFRACTION99.93
3.27-3.350.33141580.24422656X-RAY DIFFRACTION99.68
3.35-3.450.26121520.2292614X-RAY DIFFRACTION99.68
3.45-3.560.27881570.22112634X-RAY DIFFRACTION99.89
3.56-3.690.24061400.22162661X-RAY DIFFRACTION99.82
3.69-3.840.24591610.19372659X-RAY DIFFRACTION99.96
3.84-4.010.21291260.18432701X-RAY DIFFRACTION99.96
4.01-4.220.21231430.18272668X-RAY DIFFRACTION99.96
4.22-4.490.21181420.17662680X-RAY DIFFRACTION99.82
4.49-4.830.21171280.16082698X-RAY DIFFRACTION99.68
4.84-5.320.19041370.17372726X-RAY DIFFRACTION99.93
5.32-6.090.24241360.2052717X-RAY DIFFRACTION99.79
6.09-7.660.23291410.18942764X-RAY DIFFRACTION99.59
7.66-39.810.18031480.16922853X-RAY DIFFRACTION99.34

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