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- PDB-7mk8: Crystal structure of a surface mutant of human fetal-specific CYP... -

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Basic information

Entry
Database: PDB / ID: 7mk8
TitleCrystal structure of a surface mutant of human fetal-specific CYP3A7 bound to dithiothreitol
ComponentsIsoform 2 of Cytochrome P450 3A7
KeywordsOXIDOREDUCTASE / cytochrome P450 / CYP3A7 / surface mutations / dithiothreitol
Function / homology
Function and homology information


all-trans retinoic acid 18-hydroxylase activity / testosterone 6-beta-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 ...all-trans retinoic acid 18-hydroxylase activity / testosterone 6-beta-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
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 3A7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSevrioukova, I.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES025767 United States
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural Basis for the Diminished Ligand Binding and Catalytic Ability of Human Fetal-Specific CYP3A7.
Authors: Sevrioukova, I.F.
History
DepositionApr 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Cytochrome P450 3A7
B: Isoform 2 of Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0589
Polymers119,2292
Non-polymers1,8307
Water4,125229
1
B: Isoform 2 of Cytochrome P450 3A7
hetero molecules

A: Isoform 2 of Cytochrome P450 3A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0589
Polymers119,2292
Non-polymers1,8307
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_747-x+5/2,y-1/2,-z+5/21
Buried area4890 Å2
ΔGint-104 kcal/mol
Surface area39530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.290, 205.120, 156.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Isoform 2 of Cytochrome P450 3A7 / CYPIIIA7 / Cytochrome P450-HFLA / P450HLp2


Mass: 59614.305 Da / Num. of mol.: 2
Mutation: residues 3-22 deleted; R69G, C77G, K244E, K421A, K422A, K424A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P24462-2, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence details4His C-terminal tag

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, BisTris, ammonium sulphate

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 11, 2020 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→85.79 Å / Num. obs: 63247 / % possible obs: 99.5 % / Redundancy: 8.4 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.044 / Net I/σ(I): 10.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 9183 / CC1/2: 0.635 / Rpim(I) all: 0.579 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vcc

5vcc


Resolution: 2.15→49.674 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 3068 4.87 %
Rwork0.2029 59949 -
obs0.2053 63017 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.29 Å2 / Biso mean: 61.9535 Å2 / Biso min: 27.51 Å2
Refinement stepCycle: final / Resolution: 2.15→49.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7436 0 117 229 7782
Biso mean--56.75 56.86 -
Num. residues----927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077918
X-RAY DIFFRACTIONf_angle_d0.92310781
X-RAY DIFFRACTIONf_chiral_restr0.0491203
X-RAY DIFFRACTIONf_plane_restr0.0061355
X-RAY DIFFRACTIONf_dihedral_angle_d14.9334796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.18360.43711550.3844270599
2.1836-2.21940.41571220.3935267698
2.2194-2.25770.57051340.4782264697
2.2577-2.29870.39921350.3537266198
2.2987-2.34290.39931450.31822700100
2.3429-2.39070.34541450.28682709100
2.3907-2.44270.33361470.27622707100
2.4427-2.49950.37591520.2702267098
2.4995-2.56210.31961250.2425266699
2.5621-2.63130.29641190.23882765100
2.6313-2.70870.31061430.2396271799
2.7087-2.79620.30851210.246274099
2.7962-2.89610.32371370.24270899
2.8961-3.0120.2791470.22832739100
3.012-3.14910.30871610.22472724100
3.1491-3.31510.261230.2198272698
3.3151-3.52270.26151380.20392750100
3.5227-3.79460.23311590.18032748100
3.7946-4.17630.20551420.15462754100
4.1763-4.78020.18171230.1424275698
4.7802-6.0210.18441340.15822821100
6.021-49.6740.18371610.1532286198
Refinement TLS params.Method: refined / Origin x: 92.4081 Å / Origin y: 254.9387 Å / Origin z: 175.2478 Å
111213212223313233
T0.357 Å2-0.0284 Å2-0.0008 Å2-0.3639 Å2-0.0055 Å2--0.3781 Å2
L-0.1026 °20.1802 °2-0.099 °2-1.2859 °2-0.3189 °2--0.1522 °2
S-0.0298 Å °0.0061 Å °-0.0121 Å °-0.1494 Å °0.0034 Å °-0.0682 Å °0.0731 Å °-0.0228 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 497
2X-RAY DIFFRACTION1allA500 - 700
3X-RAY DIFFRACTION1allB25 - 497
4X-RAY DIFFRACTION1allB500 - 700
5X-RAY DIFFRACTION1allS1 - 230

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