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- PDB-8gk3: Cytochrome P450 3A7 in complex with Dehydroepiandrosterone sulfate -

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Basic information

Entry
Database: PDB / ID: 8gk3
TitleCytochrome P450 3A7 in complex with Dehydroepiandrosterone sulfate
ComponentsCytochrome P450 3A7
KeywordsOXIDOREDUCTASE / Monooxygenase
Function / homology
Function and homology information


all-trans retinoic acid 18-hydroxylase activity / retinoic acid 4-hydroxylase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / lipid hydroxylation / oxidative demethylation / steroid biosynthetic process / Xenobiotics / estrogen metabolic process / retinol metabolic process ...all-trans retinoic acid 18-hydroxylase activity / retinoic acid 4-hydroxylase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / lipid hydroxylation / oxidative demethylation / steroid biosynthetic process / Xenobiotics / estrogen metabolic process / retinol metabolic process / retinoic acid metabolic process / unspecific monooxygenase / aromatase activity / steroid hydroxylase activity / steroid metabolic process / xenobiotic metabolic process / monooxygenase activity / oxygen binding / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, E-class, group II / Cytochrome P450, E-class, CYP3A / 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 / 17-oxoandrost-5-en-3beta-yl hydrogen sulfate / Cytochrome P450 3A7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, J. / Scott, E.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI150494 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Human cytochrome P450 3A7 binding four copies of its native substrate dehydroepiandrosterone 3-sulfate.
Authors: Liu, J. / Kandel, S.E. / Lampe, J.N. / Scott, E.E.
History
DepositionMar 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Aug 30, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / refine / refine_ls_restr / refine_ls_shell / struct_asym / struct_conn
Item: _chem_comp.id / _chem_comp.name ..._chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_asym.entity_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Ligand geometry / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 3A7
B: Cytochrome P450 3A7
C: Cytochrome P450 3A7
D: Cytochrome P450 3A7
E: Cytochrome P450 3A7
F: Cytochrome P450 3A7
G: Cytochrome P450 3A7
H: Cytochrome P450 3A7
I: Cytochrome P450 3A7
J: Cytochrome P450 3A7
K: Cytochrome P450 3A7
L: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)680,80548
Polymers664,56412
Non-polymers16,24236
Water57632
1
A: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7344
Polymers55,3801
Non-polymers1,3533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7344
Polymers55,3801
Non-polymers1,3533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4716
Polymers55,3801
Non-polymers2,0905
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8397
Polymers55,3801
Non-polymers2,4596
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4716
Polymers55,3801
Non-polymers2,0905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9972
Polymers55,3801
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9972
Polymers55,3801
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1025
Polymers55,3801
Non-polymers1,7224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7344
Polymers55,3801
Non-polymers1,3533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7344
Polymers55,3801
Non-polymers1,3533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9972
Polymers55,3801
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9972
Polymers55,3801
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.516, 219.381, 130.447
Angle α, β, γ (deg.)90.000, 102.165, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Cytochrome P450 3A7 / CYPIIIA7 / Cytochrome P450-HFLA / P450HLp2


Mass: 55380.324 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A7 / Production host: Escherichia coli (E. coli) / References: UniProt: P24462, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical...
ChemComp-ZWY / 17-oxoandrost-5-en-3beta-yl hydrogen sulfate / Dehydroepiandrosterone sulfate / DHEA sulfate / DHEA-S


Mass: 368.488 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C19H28O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 20% (w/v) PEG 3350, 0.2 M Lithium acetate dihydrate, pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→39.94 Å / Num. obs: 190994 / % possible obs: 99.1 % / Redundancy: 7 % / Biso Wilson estimate: 68.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Net I/σ(I): 10.3
Reflection shellResolution: 2.6→2.74 Å / Num. unique obs: 27624 / CC1/2: 0.473 / Rpim(I) all: 0.878

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASER1.18.2_3874phasing
Cootmodel building
SCALAdata scaling
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.94 Å / SU ML: 0.4959 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.2787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2731 1999 1.05 %
Rwork0.2098 187688 -
obs0.2105 189687 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.63 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44268 0 1116 32 45416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011346629
X-RAY DIFFRACTIONf_angle_d1.26163555
X-RAY DIFFRACTIONf_chiral_restr0.09937112
X-RAY DIFFRACTIONf_plane_restr0.00787891
X-RAY DIFFRACTIONf_dihedral_angle_d21.81217437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.44161310.380912287X-RAY DIFFRACTION90.34
2.66-2.740.39291420.354313367X-RAY DIFFRACTION98.54
2.74-2.820.371440.332313435X-RAY DIFFRACTION98.93
2.82-2.910.35941430.303713494X-RAY DIFFRACTION99.26
2.91-3.010.37641440.28813441X-RAY DIFFRACTION98.87
3.01-3.130.36211420.288513344X-RAY DIFFRACTION98.32
3.13-3.270.31851440.269313588X-RAY DIFFRACTION99.49
3.27-3.450.33951450.256213505X-RAY DIFFRACTION99.44
3.45-3.660.31561420.231713471X-RAY DIFFRACTION99.3
3.66-3.950.27951440.209913454X-RAY DIFFRACTION98.59
3.95-4.340.26721450.179813553X-RAY DIFFRACTION99.45
4.34-4.970.21991440.164913523X-RAY DIFFRACTION99.16
4.97-6.260.23351440.18613590X-RAY DIFFRACTION99.47
6.26-39.940.2051450.15713636X-RAY DIFFRACTION98.85

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