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- PDB-8fda: Human Cytochrome P450 17A1 in complex with steroidal isonitrile i... -

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Basic information

Entry
Database: PDB / ID: 8fda
TitleHuman Cytochrome P450 17A1 in complex with steroidal isonitrile inhibitor
ComponentsSteroid 17-alpha-hydroxylase/17,20 lyase
KeywordsOXIDOREDUCTASE / Cytochrome P450 17A1 / Cytochrome P450 c17 / 17-alpha hydroxylase / 17 / 20 lyase / isonitrile / steroid
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-XPK / Steroid 17-alpha-hydroxylase/17,20 lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRichard, A.M. / Scott, E.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM130997 United States
CitationJournal: Commun Chem / Year: 2023
Title: Selective steroidogenic cytochrome P450 haem iron ligation by steroid-derived isonitriles.
Authors: Richard, A.M. / Wong, N.R. / Harris, K. / Sundar, R. / Scott, E.E. / Pochapsky, T.C.
History
DepositionDec 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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)227,57214
Polymers222,9614
Non-polymers4,61110
Water4,828268
1
A: Steroid 17-alpha-hydroxylase/17,20 lyase
B: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4286
Polymers111,4802
Non-polymers1,9484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Steroid 17-alpha-hydroxylase/17,20 lyase
C: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7867
Polymers111,4802
Non-polymers2,3065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 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)170,85811
Polymers167,2203
Non-polymers3,6378
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Steroid 17-alpha-hydroxylase/17,20 lyase
D: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7867
Polymers111,4802
Non-polymers2,3065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.130, 152.275, 171.587
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

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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 / 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 / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
References: steroid 17alpha-monooxygenase, 17alpha-hydroxyprogesterone deacetylase
#3: Chemical
ChemComp-XPK / [(1~{R})-1-[(3~{S},5~{S},8~{R},9~{S},10~{S},13~{S},17~{R})-3-methanoyloxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17-hexadecahydrocyclopenta[a]phenanthren-17-yl]ethyl]-methylidyne-azanium / 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: 357.530 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H35NO2 / Feature type: SUBJECT OF INVESTIGATION
References: steroid 17alpha-monooxygenase, 17alpha-hydroxyprogesterone deacetylase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 0.25 M LiSO4, 30% PEG 3350, and 7% sucrose

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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: Feb 19, 2022
Details: Beam focused to 50 by 15 microns, beam attenuated 96.5%
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→38.96 Å / Num. obs: 114766 / % possible obs: 99.6 % / Redundancy: 13.4 % / Biso Wilson estimate: 44.37 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.075 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 16489 / CC1/2: 0.382 / Rpim(I) all: 1.453 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.96 Å / SU ML: 0.2958 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.1554
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2594 1998 1.77 %
Rwork0.2158 111089 -
obs0.2165 113087 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14864 0 328 268 15460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004715568
X-RAY DIFFRACTIONf_angle_d0.729621167
X-RAY DIFFRACTIONf_chiral_restr0.04322400
X-RAY DIFFRACTIONf_plane_restr0.00532646
X-RAY DIFFRACTIONf_dihedral_angle_d17.90415756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.34461320.37117393X-RAY DIFFRACTION92.5
2.25-2.310.37351370.34527598X-RAY DIFFRACTION94.99
2.31-2.380.3791420.31567893X-RAY DIFFRACTION98.81
2.38-2.460.33481390.29777769X-RAY DIFFRACTION97.08
2.46-2.550.30211410.27677830X-RAY DIFFRACTION97.97
2.55-2.650.31421430.27427924X-RAY DIFFRACTION98.87
2.65-2.770.3361430.27767951X-RAY DIFFRACTION98.78
2.77-2.920.30491440.27017920X-RAY DIFFRACTION98.74
2.92-3.10.3211430.24958029X-RAY DIFFRACTION99.7
3.1-3.340.26661450.23278059X-RAY DIFFRACTION99.82
3.34-3.670.28321440.21368026X-RAY DIFFRACTION99.34
3.67-4.20.23771470.17478106X-RAY DIFFRACTION99.65
4.2-5.290.2021470.15678190X-RAY DIFFRACTION99.63
5.3-38.960.19121510.17978401X-RAY DIFFRACTION98.95

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