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- PDB-6t0j: Crystal structure of CYP124 in complex with SQ109 -

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Basic information

Entry
Database: PDB / ID: 6t0j
TitleCrystal structure of CYP124 in complex with SQ109
ComponentsMethyl-branched lipid omega-hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / CYP / SQ109 / SQ / 109 / MmpL3 / tuberculosis / mycobacterium tuberculosis / antituberculosis / drug / substrate
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
FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Chem-RWZ / Methyl-branched lipid omega-hydroxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBukhdruker, S. / Marin, E. / Varaksa, T. / Gilep, A. / Strushkevich, N. / Borshchevskiy, V.
Funding support Russian Federation, Belarus, 3items
OrganizationGrant numberCountry
Russian Foundation for Basic Research20-54-00005 Russian Federation
Belarusian Republican Foundation for Fundamental ResearchB20R-061Belarus
Ministry of Science and Higher Education of the Russian Federation075-00337-20-03 (FSMG-2020-0003) Russian Federation
CitationJournal: Int J Mol Sci / Year: 2020
Title: Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450.
Authors: Bukhdruker, S. / Varaksa, T. / Grabovec, I. / Marin, E. / Shabunya, P. / Kadukova, M. / Grudinin, S. / Kavaleuski, A. / Gusach, 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 1.1Oct 28, 2020Group: Author supporting evidence / Database references
Category: citation / pdbx_audit_support / pdbx_related_exp_data_set
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 4, 2020Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 2.0Feb 17, 2021Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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)50,50914
Polymers48,8391
Non-polymers1,67013
Water13,475748
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-30 kcal/mol
Surface area16970 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 , 7 types, 761 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-RWZ / N-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine


Mass: 330.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38N2 / 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#8: 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 0.3 M Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. obs: 162381 / % possible obs: 97.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.193 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.92-30728.919260.9970.05899.1
3.48-4.926.227.233400.9960.06196.5
2.84-3.486.723.844100.9960.07799.1
2.46-2.847.119.852100.9950.10499.2
2.2-2.466.816.758570.9920.12297.9
2.01-2.26.513.364140.9890.14797.6
1.86-2.016.810.670980.9850.18699.4
1.74-1.866.97.975840.9730.24799
1.64-1.7475.880880.9560.33498.9
1.56-1.646.34.482840.930.41596.2
1.48-1.566.73.588940.8880.53398.3
1.42-1.486.82.693510.8040.70698.9
1.36-1.426.9297500.7350.8798.6
1.32-1.366.71.699590.6831.02997.5
1.27-1.326.41.3103530.5591.25497.2
1.23-1.276.61.1107240.4751.45397.9
1.19-1.236.40.9110910.391.68697.9
1.16-1.196.20.7113350.3221.8997.2
1.13-1.165.70.6115800.2522.24696.4
1.1-1.135.70.4111330.1682.75190.9

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Processing

Software
NameVersionClassification
MxCuBE2data collection
XDS20180409data reduction
XSCALE20180409data scaling
PHASER2.8.3phasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T0F

6t0f


Resolution: 1.25→29.54 Å / SU ML: 0.1526 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1687
RfactorNum. reflection% reflection
Rfree0.1829 5509 4.96 %
Rwork0.1479 --
obs0.1496 111134 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.69 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 113 748 4231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764208
X-RAY DIFFRACTIONf_angle_d1.14285822
X-RAY DIFFRACTIONf_chiral_restr0.0739603
X-RAY DIFFRACTIONf_plane_restr0.0071784
X-RAY DIFFRACTIONf_dihedral_angle_d14.37081589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.34831700.31333215X-RAY DIFFRACTION90.22
1.27-1.280.26871810.26693520X-RAY DIFFRACTION97.7
1.28-1.30.26051750.25883475X-RAY DIFFRACTION97.28
1.3-1.310.33051790.25373468X-RAY DIFFRACTION97.36
1.31-1.330.29071900.24423399X-RAY DIFFRACTION95.25
1.33-1.350.27781610.22953581X-RAY DIFFRACTION98.4
1.35-1.370.24441780.21313507X-RAY DIFFRACTION98.58
1.37-1.390.25561880.19953528X-RAY DIFFRACTION98.57
1.39-1.410.22882150.19493516X-RAY DIFFRACTION98.7
1.41-1.430.23831970.19543554X-RAY DIFFRACTION98.87
1.43-1.460.23641830.19083525X-RAY DIFFRACTION98.85
1.46-1.480.25351780.1873550X-RAY DIFFRACTION98.86
1.48-1.510.21491840.18573537X-RAY DIFFRACTION98.75
1.51-1.540.22721990.18313526X-RAY DIFFRACTION98.08
1.54-1.580.23271860.18233500X-RAY DIFFRACTION97.59
1.58-1.610.22671810.17753400X-RAY DIFFRACTION95.04
1.61-1.650.21411850.17083502X-RAY DIFFRACTION97.82
1.65-1.70.20031940.16263531X-RAY DIFFRACTION98.83
1.7-1.750.17281960.15733549X-RAY DIFFRACTION98.97
1.75-1.80.17971910.14383539X-RAY DIFFRACTION99.1
1.8-1.870.18591650.13523603X-RAY DIFFRACTION99.18
1.87-1.940.16461770.12383579X-RAY DIFFRACTION99.63
1.94-2.030.16311970.11863569X-RAY DIFFRACTION99.08
2.03-2.140.17191950.11873520X-RAY DIFFRACTION98.07
2.14-2.270.15491650.11623455X-RAY DIFFRACTION95.51
2.27-2.450.15661800.11993589X-RAY DIFFRACTION99.37
2.45-2.70.14561840.1223608X-RAY DIFFRACTION99.35
2.7-3.080.16961970.12483551X-RAY DIFFRACTION99.05
3.08-3.890.12671750.123609X-RAY DIFFRACTION99.11
3.89-29.540.1621630.14323620X-RAY DIFFRACTION97.42

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