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- PDB-6t0g: Crystal structure of CYP124 in complex with vitamin D3 -

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Basic information

Entry
Database: PDB / ID: 6t0g
TitleCrystal structure of CYP124 in complex with vitamin D3
ComponentsMethyl-branched lipid omega-hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / CYP / vitaminD3 / D3 / vitamin / 124 / CYP124 / cholecalciferol / calciferol / 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 / TRIETHYLENE GLYCOL / Chem-VD3 / Methyl-branched lipid omega-hydroxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.3Feb 17, 2021Group: Database references / Category: citation / Item: _citation.year
Revision 1.4Jan 24, 2024Group: 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: Methyl-branched lipid omega-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1897
Polymers48,8391
Non-polymers1,3506
Water13,475748
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-28 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.540, 75.110, 56.590
Angle α, β, γ (deg.)90.000, 106.840, 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 Methyl-branched lipid omega-hydroxylase / Cholest-4-en-3-one C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25R)-3-oxocholest-4- ...Cholest-4-en-3-one C26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / Cholesterol C26-monooxygenase / Cholesterol C26-monooxygenase [(25R)-3beta-hydroxycholest-5-en-26-oate forming] / Cytochrome P450 124 / Steroid C26-monooxygenase / Steroid C27-monooxygenase


Mass: 48838.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: cyp124, Rv2266, MTCY339.44c / 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 , 5 types, 754 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-VD3 / (1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL / VITAMIN D3


Mass: 384.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.1M BisTris, 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: 0.984 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. obs: 164106 / % possible obs: 98.8 % / Redundancy: 3 % / Biso Wilson estimate: 10.83 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.195 / Net I/σ(I): 3.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.92-303.21559120.9870.08596.7
3.48-4.923.115.133570.9880.07997.4
2.84-3.483.313.843900.9870.0998.9
2.46-2.843.411.952010.9830.10899.3
2.2-2.463.210.259190.9780.12999.2
2.01-2.23.18.864260.9720.1598.3
1.86-2.013.37.371090.960.18999.7
1.74-1.863.45.875900.9310.24599.7
1.64-1.743.24.381230.9010.31299.4
1.56-1.643.13.583890.8640.37797.9
1.48-1.562.889620.8040.46799.4
1.42-1.483.22.193760.6920.6299.5
1.36-1.423.11.697870.5990.75499.5
1.31-1.363.11.3100230.5160.87998.6
1.27-1.3131.1105840.4841.01999.4
1.23-1.273.10.9108350.3591.16999.5
1.19-1.232.90.8112520.3171.29899.5
1.16-1.192.70.6112780.2521.43897
1.13-1.162.60.5116920.2011.69997.7
1.1-1.132.60.4119430.1332.01397.5

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Processing

Software
NameVersionClassification
MxCuBE2data collection
XDS20180126data reduction
XSCALE20180409data scaling
PHASER2.8.3phasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T0F

6t0f


Resolution: 1.3→19.75 Å / SU ML: 0.159 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.8375
RfactorNum. reflection% reflection
Rfree0.1903 4944 4.97 %
Rwork0.1631 --
obs0.1645 99549 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.31 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 71 748 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01183894
X-RAY DIFFRACTIONf_angle_d1.21845371
X-RAY DIFFRACTIONf_chiral_restr0.0884572
X-RAY DIFFRACTIONf_plane_restr0.0092726
X-RAY DIFFRACTIONf_dihedral_angle_d13.7411454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.33011360.27112489X-RAY DIFFRACTION77.5
1.31-1.330.26311530.26343088X-RAY DIFFRACTION97.27
1.33-1.350.28511400.24663206X-RAY DIFFRACTION98.85
1.35-1.360.27761620.24243159X-RAY DIFFRACTION99.43
1.36-1.380.26321650.24133199X-RAY DIFFRACTION99.56
1.38-1.40.29491970.23413184X-RAY DIFFRACTION99.56
1.4-1.420.24921760.21663124X-RAY DIFFRACTION99.43
1.42-1.440.23461820.21433159X-RAY DIFFRACTION99.64
1.44-1.460.26491590.21643195X-RAY DIFFRACTION99.73
1.46-1.490.25421690.20023167X-RAY DIFFRACTION99.43
1.49-1.510.22731610.18183185X-RAY DIFFRACTION99.52
1.51-1.540.22081780.18153183X-RAY DIFFRACTION99.35
1.54-1.570.22841710.1783191X-RAY DIFFRACTION98.91
1.57-1.60.2111620.17183043X-RAY DIFFRACTION96.86
1.6-1.640.19821520.16353159X-RAY DIFFRACTION98.31
1.64-1.680.22081820.16493175X-RAY DIFFRACTION99.17
1.68-1.720.21491760.1683207X-RAY DIFFRACTION99.47
1.72-1.760.19731650.15733158X-RAY DIFFRACTION99.76
1.76-1.820.19151830.15093171X-RAY DIFFRACTION99.79
1.82-1.870.18311420.13893226X-RAY DIFFRACTION99.76
1.87-1.940.18161590.13793223X-RAY DIFFRACTION99.85
1.94-2.020.17431580.13743218X-RAY DIFFRACTION99.7
2.02-2.110.15091890.13813147X-RAY DIFFRACTION99.67
2.11-2.220.16451490.13443149X-RAY DIFFRACTION97.26
2.22-2.360.17341580.13943216X-RAY DIFFRACTION99.68
2.36-2.540.16211720.15233166X-RAY DIFFRACTION99.26
2.54-2.80.18011780.15523188X-RAY DIFFRACTION99.47
2.8-3.20.17331700.15813207X-RAY DIFFRACTION99.06
3.2-4.030.15031580.1533181X-RAY DIFFRACTION98.03
4.03-19.750.17011420.16023242X-RAY DIFFRACTION97.69

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