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- PDB-3s79: Human placental aromatase cytochrome P450 (CYP19A1) refined at 2.... -

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Basic information

Entry
Database: PDB / ID: 3s79
TitleHuman placental aromatase cytochrome P450 (CYP19A1) refined at 2.75 angstrom
ComponentsCytochrome P450 19A1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process ...aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process / sterol metabolic process / prostate gland growth / negative regulation of macrophage chemotaxis / mammary gland development / steroid biosynthetic process / steroid hydroxylase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / aromatase activity / female gonad development / uterus development / Endogenous sterols / oxygen binding / response to estradiol / electron transfer activity / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
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
4-ANDROSTENE-3-17-DIONE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Aromatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Refinement at higher resolution / Resolution: 2.75 Å
AuthorsGhosh, D.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Novel aromatase inhibitors by structure-guided design.
Authors: Ghosh, D. / Lo, J. / Morton, D. / Valette, D. / Xi, J. / Griswold, J. / Hubbell, S. / Egbuta, C. / Jiang, W. / An, J. / Davies, H.M.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Cytochrome P450 19A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1436
Polymers57,9551
Non-polymers1,1885
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.218, 140.218, 119.271
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytochrome P450 19A1 / Aromatase / CYPXIX / Cytochrome P-450AROM / Estrogen synthase


Mass: 57954.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP19A1, ARO1, CYAR, CYP19 / Production host: Escherichia coli (E. coli) / References: UniProt: P11511, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE / Androstenedione


Mass: 286.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20-30% PEG 4000, phosphate buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→121.43 Å / Num. all: 33618 / Num. obs: 33618 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 83.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.42
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.75-2.851100
2.85-2.961100
2.96-3.11100
3.1-3.261100
3.26-3.461100
3.46-3.73199.9
3.73-4.111100
4.11-4.71100
4.7-5.921100
5.92-50195.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Refinement at higher resolution
Starting model: PDB ENTRY 3EQM

3eqm


Resolution: 2.75→121.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.232 / SU ML: 0.177 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 1769 5 %RANDOM
Rwork0.21965 ---
all0.22047 33618 --
obs0.22047 33618 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.152 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å21.12 Å2-0 Å2
2--2.24 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.75→121.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 79 37 3774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223835
X-RAY DIFFRACTIONr_angle_refined_deg1.2722.0155192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82823.554166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.18915712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2051525
X-RAY DIFFRACTIONr_chiral_restr0.1010.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212822
X-RAY DIFFRACTIONr_mcbond_it0.4551.52257
X-RAY DIFFRACTIONr_mcangle_it0.8823670
X-RAY DIFFRACTIONr_scbond_it1.0431578
X-RAY DIFFRACTIONr_scangle_it1.8514.51522
LS refinement shellResolution: 2.75→2.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 114 -
Rwork0.351 2458 -
obs--99.04 %

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