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- PDB-6ww0: Human steroidogenic cytochrome P450 17A1 with 3-keto-5alpha-abira... -

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Basic information

Entry
Database: PDB / ID: 6ww0
TitleHuman steroidogenic cytochrome P450 17A1 with 3-keto-5alpha-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 ...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 / 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-UDJ / Steroid 17-alpha-hydroxylase/17,20 lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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)R01 GM102505 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
DepositionMay 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 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)226,89514
Polymers222,9614
Non-polymers3,93510
Water17,421967
1
A: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7063
Polymers55,7401
Non-polymers9662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7063
Polymers55,7401
Non-polymers9662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7063
Polymers55,7401
Non-polymers9662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7775
Polymers55,7401
Non-polymers1,0374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.722, 151.182, 169.944
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 273 or resid 285 through 503 or resid 600 through 601))A31 - 273
121(chain 'A' and (resid 31 through 273 or resid 285 through 503 or resid 600 through 601))A285 - 503
131(chain 'A' and (resid 31 through 273 or resid 285 through 503 or resid 600 through 601))A600 - 601
241(chain 'B' and (resid 31 through 503 or resid 600 through 601))B31 - 273
251(chain 'B' and (resid 31 through 503 or resid 600 through 601))B285 - 503
261(chain 'B' and (resid 31 through 503 or resid 600 through 601))B600 - 601
371(chain 'C' and (resid 31 through 273 or resid 285 through 503 or resid 600 through 601))C31 - 273
381(chain 'C' and (resid 31 through 273 or resid 285 through 503 or resid 600 through 601))C285 - 503
391(chain 'C' and (resid 31 through 273 or resid 285 through 503 or resid 600 through 601))C600 - 601
4101(chain 'D' and (resid 31 through 273 or resid 285 through 503 or resid 600 through 601))D31 - 273
4111(chain 'D' and (resid 31 through 273 or resid 285 through 503 or resid 600 through 601))D285 - 503
4121(chain 'D' and (resid 31 through 273 or resid 285 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-UDJ / (5alpha,8alpha)-17-(pyridin-3-yl)androst-16-en-3-one / 3-Keto-5α-abiraterone


Mass: 349.509 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H31NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 175 mM Tris HCl (pH = 8.5), 30% PEG 3350, 300 mM LiSO4, 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: 0.979531 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979531 Å / Relative weight: 1
ReflectionResolution: 2→38.68 Å / Num. obs: 146679 / % possible obs: 98.8 % / Redundancy: 10.3 % / Biso Wilson estimate: 28.12 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.066 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 20040 / CC1/2: 0.486 / Rpim(I) all: 0.717 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IRQ

5irq


Resolution: 2.01→38.68 Å / SU ML: 0.2038 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2184 7240 5.01 %
Rwork0.1854 137318 -
obs0.1871 144558 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.58 Å2
Refinement stepCycle: LAST / Resolution: 2.01→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14879 0 278 967 16124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01415521
X-RAY DIFFRACTIONf_angle_d1.346521093
X-RAY DIFFRACTIONf_chiral_restr0.07072370
X-RAY DIFFRACTIONf_plane_restr0.00982655
X-RAY DIFFRACTIONf_dihedral_angle_d17.81785759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.34121310.29972691X-RAY DIFFRACTION58.41
2.03-2.060.31362360.29084582X-RAY DIFFRACTION99.24
2.06-2.080.43172240.36294551X-RAY DIFFRACTION98.29
2.08-2.110.27432250.23574618X-RAY DIFFRACTION99.73
2.11-2.130.2642430.22094622X-RAY DIFFRACTION99.84
2.13-2.160.2612390.21354612X-RAY DIFFRACTION99.77
2.16-2.190.24562530.21034579X-RAY DIFFRACTION98.96
2.19-2.230.28352650.21654565X-RAY DIFFRACTION98.93
2.23-2.260.33742110.26554533X-RAY DIFFRACTION97.21
2.26-2.30.25962320.20354614X-RAY DIFFRACTION99.61
2.3-2.340.2452510.19664529X-RAY DIFFRACTION99.23
2.34-2.380.19732660.18944639X-RAY DIFFRACTION99.67
2.38-2.430.23342600.19014576X-RAY DIFFRACTION99.79
2.43-2.480.25952840.17964606X-RAY DIFFRACTION99.84
2.48-2.530.21812380.17864642X-RAY DIFFRACTION99.75
2.53-2.590.22482030.17764677X-RAY DIFFRACTION99.92
2.59-2.650.24912430.1914613X-RAY DIFFRACTION99.77
2.65-2.730.24162430.20394636X-RAY DIFFRACTION99.69
2.73-2.810.22032490.18354661X-RAY DIFFRACTION99.86
2.81-2.90.2282470.18544651X-RAY DIFFRACTION99.98
2.9-30.27012410.19554634X-RAY DIFFRACTION99.27
3-3.120.24152390.17984635X-RAY DIFFRACTION99.47
3.12-3.260.20542590.16964668X-RAY DIFFRACTION99.9
3.26-3.430.2112300.17924694X-RAY DIFFRACTION99.74
3.43-3.650.19432410.16834681X-RAY DIFFRACTION99.92
3.65-3.930.17482510.15784711X-RAY DIFFRACTION99.88
3.93-4.330.16852490.1494729X-RAY DIFFRACTION99.76
4.33-4.950.16252720.14244651X-RAY DIFFRACTION98.84
4.95-6.230.21182620.17954798X-RAY DIFFRACTION99.94
6.23-38.680.19022530.19064920X-RAY DIFFRACTION98.57

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