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- PDB-4nky: Human steroidogenic cytochrome P450 17A1 mutant A105L with substr... -

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Basic information

Entry
Database: PDB / ID: 4nky
TitleHuman steroidogenic cytochrome P450 17A1 mutant A105L with substrate 17alpha-hydroxyprogesterone
ComponentsSteroid 17-alpha-hydroxylase/17,20 lyase
KeywordsOXIDOREDUCTASE / LYASE / heme protein / monooxygenase / steroid 17alpha-hydroxylase / steroid C17 / 20 lyase / NADPH-cytochrome P450 reductase / cytochrome b5 / endoplasmic reticulum membrane
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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(9beta)-17-hydroxypregn-4-ene-3,20-dione / PROTOPORPHYRIN IX CONTAINING FE / Steroid 17-alpha-hydroxylase/17,20 lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsScott, E.E. / Petrunak, E.M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structures of Human Steroidogenic Cytochrome P450 17A1 with Substrates.
Authors: Petrunak, E.M. / DeVore, N.M. / Porubsky, P.R. / Scott, E.E.
History
DepositionNov 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)226,91712
Polymers223,1294
Non-polymers3,7888
Water2,900161
1
A: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7293
Polymers55,7821
Non-polymers9472
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)56,7293
Polymers55,7821
Non-polymers9472
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)56,7293
Polymers55,7821
Non-polymers9472
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)56,7293
Polymers55,7821
Non-polymers9472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.285, 151.778, 168.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 55782.223 Da / Num. of mol.: 4 / Fragment: UNP residues 24-508 / Mutation: A105L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP17, CYP17A1, S17AH / Plasmid: pCWori17A1delta19H / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P05093, EC: 1.14.99.9, EC: 4.1.2.30
#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-3QZ / (9beta)-17-hydroxypregn-4-ene-3,20-dione / 17α-Hydroxyprogesterone


Mass: 330.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30O3 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 175 mM Tris-HCl, 250 mM lithium sulfate, 30% PEG3350, 3% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2013 / Details: Rh coated mirror, K-B focusing mirror
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→39.153 Å / Num. obs: 76008 / % possible obs: 99.1 % / Redundancy: 6.7 %
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.7 % / % possible all: 95.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SWZ

3swz


Resolution: 2.55→39.153 Å / SU ML: 0.33 / σ(F): 1.33 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 3806 5.02 %
Rwork0.1782 --
obs0.1816 75825 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→39.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14832 0 268 161 15261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715459
X-RAY DIFFRACTIONf_angle_d1.22621015
X-RAY DIFFRACTIONf_dihedral_angle_d14.3445752
X-RAY DIFFRACTIONf_chiral_restr0.1032367
X-RAY DIFFRACTIONf_plane_restr0.0042646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.58240.32031100.26182232X-RAY DIFFRACTION83
2.5824-2.61640.32171580.26082631X-RAY DIFFRACTION99
2.6164-2.65230.30111500.25062630X-RAY DIFFRACTION99
2.6523-2.69010.32931120.25162691X-RAY DIFFRACTION100
2.6901-2.73030.3361330.24662646X-RAY DIFFRACTION99
2.7303-2.77290.32721360.24192693X-RAY DIFFRACTION100
2.7729-2.81840.32271640.24172595X-RAY DIFFRACTION99
2.8184-2.8670.29391300.23172674X-RAY DIFFRACTION100
2.867-2.91910.33271490.21822633X-RAY DIFFRACTION100
2.9191-2.97520.31191440.22172682X-RAY DIFFRACTION100
2.9752-3.03590.29161570.22242662X-RAY DIFFRACTION100
3.0359-3.10190.34021280.21052658X-RAY DIFFRACTION100
3.1019-3.1740.27391530.20382668X-RAY DIFFRACTION100
3.174-3.25340.29441300.19272691X-RAY DIFFRACTION100
3.2534-3.34130.23521210.19342691X-RAY DIFFRACTION100
3.3413-3.43960.2841350.19022678X-RAY DIFFRACTION99
3.4396-3.55050.29061620.19412666X-RAY DIFFRACTION99
3.5505-3.67730.25931320.17612665X-RAY DIFFRACTION100
3.6773-3.82440.26121430.16252707X-RAY DIFFRACTION100
3.8244-3.99830.21381510.15032680X-RAY DIFFRACTION100
3.9983-4.20890.18241100.1462739X-RAY DIFFRACTION100
4.2089-4.47220.20141420.14892675X-RAY DIFFRACTION99
4.4722-4.8170.17981290.1412689X-RAY DIFFRACTION98
4.817-5.30070.22051470.14622724X-RAY DIFFRACTION100
5.3007-6.06520.24491670.17792731X-RAY DIFFRACTION100
6.0652-7.63230.2281530.18522746X-RAY DIFFRACTION99
7.6323-39.15750.18131600.14662842X-RAY DIFFRACTION98

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