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- PDB-6b82: Zebra Fish CYP-450 17A1 Mutant Abiraterone Complex -

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Basic information

Entry
Database: PDB / ID: 6b82
TitleZebra Fish CYP-450 17A1 Mutant Abiraterone Complex
ComponentsCytochrome P450, family 17, subfamily A, polypeptide 1
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / CYP17A1 mutant / P450 17A1 / MONOOXYGENASE / 17A-HYDROXYLASE / HEME PROTEIN / CYTOCHROME P450 OXIDOREDUCTASE / ABIRATERONE / 17A-HYDROXYLATION / MEMBRANE / MICROSOME / ENDOPLASMIC RETICULUM
Function / homology
Function and homology information


Androgen biosynthesis / Glucocorticoid biosynthesis / androst-4-ene-3,17-dione biosynthetic process / female sex determination / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / : / hormone biosynthetic process ...Androgen biosynthesis / Glucocorticoid biosynthesis / androst-4-ene-3,17-dione biosynthetic process / female sex determination / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / : / hormone biosynthetic process / sex differentiation / progesterone metabolic process / male sex determination / iron ion binding / heme binding / membrane
Similarity search - Function
Steroid 17-alpha-hydroxylase/17,20 lyase / 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
ACETATE ION / Abiraterone / PROTOPORPHYRIN IX CONTAINING FE / 17-alpha-hydroxyprogesterone aldolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM103937 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Inherent steroid 17 alpha ,20-lyase activity in defunct cytochrome P450 17A enzymes.
Authors: Gonzalez, E. / Johnson, K.M. / Pallan, P.S. / Phan, T.T.N. / Zhang, W. / Lei, L. / Wawrzak, Z. / Yoshimoto, F.K. / Egli, M. / Guengerich, F.P.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450, family 17, subfamily A, polypeptide 1
B: Cytochrome P450, family 17, subfamily A, polypeptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,14611
Polymers114,9422
Non-polymers2,2049
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-72 kcal/mol
Surface area37190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.920, 104.920, 235.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450, family 17, subfamily A, polypeptide 1


Mass: 57471.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Zebrafish quintuple mutant 17A1 CYP450 / Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cyp17a1 / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A2ATX9

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Non-polymers , 5 types, 43 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-AER / Abiraterone / (3S,8R,9S,10R,13S,14S)-10,13-dimethyl-17-pyridin-3-yl-2,3,4,7,8,9,11,12,14,15-decahydro-1H-cyclopenta[a]phenanthren-3-ol


Mass: 349.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H31NO / Comment: medication*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / Details: rfere

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.03→51.26 Å / Num. obs: 26303 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.047 / Rrim(I) all: 0.128 / Net I/σ(I): 14
Reflection shellResolution: 3.03→3.11 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 2 / Num. unique obs: 1896 / Rpim(I) all: 0.371 / Rrim(I) all: 1.03 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R1Z

4r1z


Resolution: 3.03→51.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.251 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25498 1330 5.1 %RANDOM
Rwork0.19295 ---
obs0.19611 24918 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.028 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å2-0 Å2-0 Å2
2--2.24 Å2-0 Å2
3----4.48 Å2
Refinement stepCycle: 1 / Resolution: 3.03→51.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7390 0 155 34 7579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197721
X-RAY DIFFRACTIONr_bond_other_d0.0020.027299
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.99810479
X-RAY DIFFRACTIONr_angle_other_deg1.03316956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59323.926326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.422151374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6441549
X-RAY DIFFRACTIONr_chiral_restr0.0880.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218427
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021540
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_it4.8267.6763741
X-RAY DIFFRACTIONr_mcbond_other4.8027.6753736
X-RAY DIFFRACTIONr_mcangle_it7.31711.5244666
X-RAY DIFFRACTIONr_mcangle_other7.31611.5254667
X-RAY DIFFRACTIONr_scbond_it5.0387.9653980
X-RAY DIFFRACTIONr_scbond_other5.0387.9663981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.73311.7595814
X-RAY DIFFRACTIONr_long_range_B_refined10.49489.9328677
X-RAY DIFFRACTIONr_long_range_B_other10.49489.9378678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.03→3.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 99 -
Rwork0.301 1793 -
obs--99.68 %

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