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- PDB-3eqm: Crystal structure of human placental aromatase cytochrome P450 in... -

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Basic information

Entry
Database: PDB / ID: 3eqm
TitleCrystal structure of human placental aromatase cytochrome P450 in complex with androstenedione
ComponentsCytochrome P450 19A1
KeywordsOXIDOREDUCTASE / Human Aromatase / Cytochrome P450 / Membrane Protein / Microsomal / Estrogen / Biosynthesis of Steroid Hormone / Disease mutation / Heme / Iron / Metal-binding / Monooxygenase / Phosphoprotein
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGhosh, D.
CitationJournal: Nature / Year: 2009
Title: Structural basis for androgen specificity and oestrogen synthesis in human aromatase.
Authors: Ghosh, D. / Griswold, J. / Erman, M. / Pangborn, W.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)59,0485
Polymers57,9551
Non-polymers1,0934
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.208, 140.208, 119.266
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 / Estrogen synthetase / P-450AROM


Mass: 57954.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: placenta / 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.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 5.84 Å3/Da / Density % sol: 78.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.4
Details: Freshly purified aromatase in 100mM potassium phosphate buffer, pH 7.4, containing 20% glycerol, 0.1mM androstenedione, and 1mM n-dodecyl-D-maltopyranoside (BDM) was mixed with reservoir ...Details: Freshly purified aromatase in 100mM potassium phosphate buffer, pH 7.4, containing 20% glycerol, 0.1mM androstenedione, and 1mM n-dodecyl-D-maltopyranoside (BDM) was mixed with reservoir cocktails of 24 to 30% polyethylene glycol 4000 and 0.5M NaCl in 0.05M Tris-HCl buffer pH 8.5 and vapor diffused in sealed 24-well sitting drop plates against corresponding reservoir solution. The purification and crystallization experiments were all conducted at 4 C. Reddish-brown color hexagonal rod-shaped crystals appeared in 7-10 days and continued to grow up to 14-16 days, VAPOR DIFFUSION, 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: 2.897→121.27 Å / Num. all: 30371 / Num. obs: 28808 / % possible obs: 99.51 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.897→2.972 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 31.1 / Num. unique all: 30371 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→37.77 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.2 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.33 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24439 1532 5 %RANDOM
Rwork0.21372 ---
obs0.21526 28808 99.39 %-
all-30371 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.281 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å21.44 Å20 Å2
2--2.89 Å20 Å2
3----4.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 74 35 3767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223819
X-RAY DIFFRACTIONr_angle_refined_deg1.3212.0165168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6923.576165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.15215711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3161525
X-RAY DIFFRACTIONr_chiral_restr0.1020.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022808
X-RAY DIFFRACTIONr_nbd_refined0.2190.21874
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.24
X-RAY DIFFRACTIONr_mcbond_it0.4721.52291
X-RAY DIFFRACTIONr_mcangle_it0.8823659
X-RAY DIFFRACTIONr_scbond_it1.00731693
X-RAY DIFFRACTIONr_scangle_it1.7124.51507
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 128 -
Rwork0.315 2106 -
obs--99.51 %

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