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- PDB-6t0h: Crystal structure of CYP124 in complex with 1-alpha-hydroxy-vitamin D3 -

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Basic information

Entry
Database: PDB / ID: 6t0h
TitleCrystal structure of CYP124 in complex with 1-alpha-hydroxy-vitamin D3
ComponentsCYP124 in complex with inhibitor carbethoxyhexyl imidazole
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / CYP / 124 / CYP124 / vitamin / D3 / vitaminD3 / 1 alpha-hydroxy / 1-alpha-hydroxy / alfacalcidol / calciferol / cholecalciferol / 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 / 1-alpha-hydroxy-vitamin D3 / TRIETHYLENE GLYCOL / 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 / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / pdbx_nonpoly_scheme
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
Revision 2.1Jan 25, 2023Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)51,28018
Polymers48,8391
Non-polymers2,44217
Water13,061725
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-29 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.560, 74.970, 56.630
Angle α, β, γ (deg.)90.000, 106.952, 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, methyl-branched lipid omega-hydroxylase, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming]

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Non-polymers , 7 types, 742 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-M9B / 1-alpha-hydroxy-vitamin D3


Mass: 400.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O2 / 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 43.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.1M Bis-Tris, 0.2M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.05→20 Å / Num. obs: 186877 / % possible obs: 97.6 % / Redundancy: 3 % / Biso Wilson estimate: 10.87 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.12 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.7-203.314.221590.9850.08997.7
3.32-4.73.213.939180.9890.08198.1
2.71-3.323.313.550470.9880.08598.9
2.35-2.713.312.859900.9860.09399.2
2.1-2.353.111.867680.9840.09998.5
1.92-2.1310.674410.9840.1198.8
1.77-1.923.29.881420.9790.12699.5
1.66-1.773.38.887710.9760.14599.7
1.57-1.663.27.693480.970.16199.8
1.48-1.573.16.798890.9640.18499.6
1.42-1.483.35.8103300.9520.22399.6
1.36-1.423.35107980.9360.26299.3
1.3-1.363.24.3112170.9180.29898.7
1.26-1.33.13.6115310.8920.34698.1
1.21-1.263.13.3118770.8610.39597.4
1.17-1.2132.9122750.8260.4397.6
1.14-1.172.82.5126730.7790.48497.3
1.11-1.142.62.1129380.7370.55696.3
1.08-1.112.71.6132120.6140.70596
1.05-1.082.41.2125530.4970.86589

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Processing

Software
NameVersionClassification
MxCuBE2data collection
XDS20190315data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T0F

6t0f


Resolution: 1.18→19.72 Å / SU ML: 0.1406 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0532
RfactorNum. reflection% reflection
Rfree0.1808 6513 4.96 %
Rwork0.1555 --
obs0.1568 131233 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.17 Å2
Refinement stepCycle: LAST / Resolution: 1.18→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 145 725 4247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794424
X-RAY DIFFRACTIONf_angle_d1.17156092
X-RAY DIFFRACTIONf_chiral_restr0.0739639
X-RAY DIFFRACTIONf_plane_restr0.0081828
X-RAY DIFFRACTIONf_dihedral_angle_d16.12731688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.32712170.3324158X-RAY DIFFRACTION97.09
1.19-1.210.30492160.31484125X-RAY DIFFRACTION97.22
1.21-1.220.28612140.30394117X-RAY DIFFRACTION96.63
1.22-1.240.31632150.29294111X-RAY DIFFRACTION96.5
1.24-1.250.30882160.27554119X-RAY DIFFRACTION96.63
1.25-1.270.28682160.27284143X-RAY DIFFRACTION97.21
1.27-1.290.27492180.26414167X-RAY DIFFRACTION96.88
1.29-1.310.25682090.2534086X-RAY DIFFRACTION97.39
1.31-1.330.25952230.25774150X-RAY DIFFRACTION97.37
1.33-1.350.28871970.25724193X-RAY DIFFRACTION97.49
1.35-1.370.26892130.22944210X-RAY DIFFRACTION97.96
1.37-1.40.26012430.22614160X-RAY DIFFRACTION97.52
1.4-1.430.24292340.20664107X-RAY DIFFRACTION97.53
1.43-1.460.22192240.18444184X-RAY DIFFRACTION98.02
1.46-1.490.18692160.17494126X-RAY DIFFRACTION97.44
1.49-1.520.17872210.16094157X-RAY DIFFRACTION97.31
1.52-1.560.17042230.15124172X-RAY DIFFRACTION97.26
1.56-1.60.19152170.14794149X-RAY DIFFRACTION97.35
1.6-1.650.18912140.14534181X-RAY DIFFRACTION97.32
1.65-1.70.16622320.14164141X-RAY DIFFRACTION97.26
1.7-1.760.17692200.13884123X-RAY DIFFRACTION97.12
1.76-1.830.17862190.13654168X-RAY DIFFRACTION96.95
1.83-1.920.16482020.13384168X-RAY DIFFRACTION97.2
1.92-2.020.17732030.13384165X-RAY DIFFRACTION96.47
2.02-2.140.15032340.13814046X-RAY DIFFRACTION95.37
2.14-2.310.1551940.13374133X-RAY DIFFRACTION96.37
2.31-2.540.15362160.144193X-RAY DIFFRACTION97.35
2.54-2.910.16732350.13434183X-RAY DIFFRACTION97.64
2.91-3.660.13912080.11824228X-RAY DIFFRACTION97.52
3.66-19.720.15162040.1324357X-RAY DIFFRACTION98.92

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