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- PDB-6t0k: Crystal structure of CYP124 in complex with inhibitor carbethoxyh... -

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Basic information

Entry
Database: PDB / ID: 6t0k
TitleCrystal structure of CYP124 in complex with inhibitor carbethoxyhexyl imidazole
ComponentsCYP124 in complex with inhibitor carbethoxyhexyl imidazole
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / CYP / CYP124 / 124 / imidazole / carbethoxy / hexyl / carbethoxyhexyl / CHImi / inhibition / tuberculosis / mycobacterium tuberculosis
Function / homology
Function and homology information


methyl-branched lipid omega-hydroxylase / methyl-branched fatty acid metabolic process / cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / fatty acid omega-oxidation / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / NADPH binding / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / ethyl 7-imidazol-1-ylheptanoate / Methyl-branched lipid omega-hydroxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsBukhdruker, S. / Marin, E. / Varaksa, T. / Gilep, A. / Strushkevich, N. / Borshchevskiy, V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-54-00030 Russian Federation
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis.
Authors: Varaksa, T. / Bukhdruker, S. / Grabovec, I. / Marin, E. / Kavaleuski, A. / Gusach, A. / Kovalev, K. / Maslov, I. / Luginina, A. / Zabelskii, D. / Astashkin, R. / Shevtsov, M. / Smolskaya, S. ...Authors: Varaksa, T. / Bukhdruker, S. / Grabovec, I. / Marin, E. / Kavaleuski, A. / Gusach, A. / Kovalev, K. / Maslov, I. / Luginina, A. / Zabelskii, D. / Astashkin, R. / Shevtsov, M. / Smolskaya, S. / Kavaleuskaya, A. / Shabunya, P. / Baranovsky, A. / Dolgopalets, V. / Charnou, Y. / Savachka, A. / Litvinovskaya, R. / Hurski, A. / Shevchenko, E. / Rogachev, A. / Mishin, A. / Gordeliy, V. / Gabrielian, A. / Hurt, D.E. / Nikonenko, B. / Majorov, K. / Apt, A. / Rosenthal, A. / Gilep, A. / Borshchevskiy, V. / Strushkevich, N.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Feb 17, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / pdbx_nonpoly_scheme / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _citation.year / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1Jan 25, 2023Group: Database references / Experimental preparation / Category: database_2 / exptl_crystal_grow
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.pH
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYP124 in complex with inhibitor carbethoxyhexyl imidazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,13210
Polymers48,8391
Non-polymers1,2939
Water11,980665
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-46 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.620, 75.030, 56.520
Angle α, β, γ (deg.)90.000, 106.923, 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

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Protein , 1 types, 1 molecules A

#1: Protein CYP124 in complex with inhibitor carbethoxyhexyl imidazole


Mass: 48838.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP3

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Non-polymers , 6 types, 674 molecules

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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-M65 / ethyl 7-imidazol-1-ylheptanoate


Mass: 224.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.1 M BisTris, 0.2 M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.06→30 Å / Num. obs: 183003 / % possible obs: 98.3 % / Redundancy: 3 % / Biso Wilson estimate: 11.57 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.11 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.74-303.123.120970.9940.06197.3
3.35-4.743.22338270.9950.05598.8
2.74-3.353.521.449340.9950.05899.3
2.37-2.743.418.558520.9940.06499.4
2.12-2.373.216.465860.9940.0799.1
1.94-2.123.31472740.9910.08399.3
1.79-1.943.411.479560.9870.10999.6
1.68-1.793.38.885090.9760.14899.6
1.58-1.683.27.190750.9660.18699.5
1.5-1.583.25.795550.9450.24199.6
1.43-1.53.34.3100880.9070.32899.6
1.37-1.433.13104730.8390.46499.1
1.31-1.373.12.4107930.7750.57798.3
1.27-1.313.11.9113760.6860.71399.1
1.22-1.273.11.6117740.5870.86499.2
1.19-1.222.91.2121390.5151.00299
1.15-1.192.81121940.3591.1896.9
1.12-1.152.70.7127730.31.44597.8
1.09-1.122.60.5131350.1981.84298.5
1.06-1.092.20.4125930.1232.34891.2

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Processing

Software
NameVersionClassification
MxCuBE2data collection
XDS20171218data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T0F

6t0f


Resolution: 1.18→29.52 Å / SU ML: 0.1251 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.5
RfactorNum. reflection% reflection
Rfree0.1564 6629 4.97 %
Rwork0.1308 --
obs0.1321 133369 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.36 Å2
Refinement stepCycle: LAST / Resolution: 1.18→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 84 665 4130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714396
X-RAY DIFFRACTIONf_angle_d0.89216098
X-RAY DIFFRACTIONf_chiral_restr0.0803627
X-RAY DIFFRACTIONf_plane_restr0.0065849
X-RAY DIFFRACTIONf_dihedral_angle_d16.61371666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.32021720.29533530X-RAY DIFFRACTION81.99
1.19-1.210.29352120.28174236X-RAY DIFFRACTION99.24
1.21-1.220.2712550.26154193X-RAY DIFFRACTION99.22
1.22-1.240.25532200.24694213X-RAY DIFFRACTION99.28
1.24-1.250.24962210.23974242X-RAY DIFFRACTION99.35
1.25-1.270.25772130.23984213X-RAY DIFFRACTION99.28
1.27-1.290.26962430.22544261X-RAY DIFFRACTION99.32
1.29-1.310.25622030.21994196X-RAY DIFFRACTION99.43
1.31-1.330.22252190.21374223X-RAY DIFFRACTION98.47
1.33-1.350.25922090.19414219X-RAY DIFFRACTION98.69
1.35-1.370.22672150.19014269X-RAY DIFFRACTION99.25
1.37-1.40.21352460.18434225X-RAY DIFFRACTION99.18
1.4-1.430.20712350.17374184X-RAY DIFFRACTION99.21
1.43-1.460.18722210.15454241X-RAY DIFFRACTION99.58
1.46-1.490.17362300.12974260X-RAY DIFFRACTION99.62
1.49-1.520.1512180.11574248X-RAY DIFFRACTION99.53
1.52-1.560.14822290.10884268X-RAY DIFFRACTION99.76
1.56-1.60.14342260.10294232X-RAY DIFFRACTION99.46
1.6-1.650.14482170.10134274X-RAY DIFFRACTION99.51
1.65-1.70.13062430.10284224X-RAY DIFFRACTION99.67
1.7-1.760.13962250.10334276X-RAY DIFFRACTION99.78
1.76-1.830.1372280.10374260X-RAY DIFFRACTION99.73
1.83-1.920.1422050.1044269X-RAY DIFFRACTION99.67
1.92-2.020.13072080.10144316X-RAY DIFFRACTION99.45
2.02-2.140.1272460.10664206X-RAY DIFFRACTION99.49
2.14-2.310.13712000.11054244X-RAY DIFFRACTION99.04
2.31-2.540.13222210.1154304X-RAY DIFFRACTION99.69
2.54-2.910.14062390.12064257X-RAY DIFFRACTION99.49
2.91-3.660.12232110.11124311X-RAY DIFFRACTION99.23
3.66-29.520.1441990.12784346X-RAY DIFFRACTION98.55

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