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- PDB-7qjl: Crystal structure of CYP142 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 7qjl
TitleCrystal structure of CYP142 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / P450 / Complex / Inhibitor / TB / Tuberculosis / cholesterol / Cytochrome / Heme
Function / homology
Function and homology information


cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / peptidoglycan-based cell wall / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
ACETATE ION / BROMIDE ION / ethyl 5-pyridin-4-yl-1~{H}-indole-2-carboxylate / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsSnee, M. / Levy, C. / Katariya, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Chemistry / Year: 2023
Title: Structure Based Discovery of Inhibitors of CYP125 and CYP142 from Mycobacterium tuberculosis.
Authors: Katariya, M.M. / Snee, M. / Tunnicliffe, R.B. / Kavanagh, M.E. / Boshoff, H.I.M. / Amadi, C.N. / Levy, C.W. / Munro, A.W. / Abell, C. / Leys, D. / Coyne, A.G. / McLean, K.J.
History
DepositionDec 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3Feb 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: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6338
Polymers44,3711
Non-polymers1,2617
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-27 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.522, 66.170, 130.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Steroid C26-monooxygenase / 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 142 / Steroid C27-monooxygenase


Mass: 44371.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp142, cyp142A1, Rv3518c, MTV023.25c / Plasmid: Pet21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P9WPL5, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming]

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Non-polymers , 5 types, 499 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-DQE / ethyl 5-pyridin-4-yl-1~{H}-indole-2-carboxylate


Mass: 266.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 8% w/v PEG 20,000, 8% v/v PEG 550 MME, 0.1M Sodium acetate pH 4.5, 0.25M KBr
Temp details: 4C

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.38→66.17 Å / Num. obs: 99205 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.035 / Net I/σ(I): 8.2
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.509 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4848 / CC1/2: 0.527 / Rpim(I) all: 0.636 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XKR

2xkr


Resolution: 1.38→51.06 Å / SU ML: 0.1346 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.6389
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1705 4859 4.9 %Random selection by FreerFlag
Rwork0.1497 94235 --
obs0.1507 99094 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.85 Å2
Refinement stepCycle: LAST / Resolution: 1.38→51.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 71 492 3657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133403
X-RAY DIFFRACTIONf_angle_d1.38224666
X-RAY DIFFRACTIONf_chiral_restr0.1022511
X-RAY DIFFRACTIONf_plane_restr0.017624
X-RAY DIFFRACTIONf_dihedral_angle_d8.6435497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.27881590.27493080X-RAY DIFFRACTION99.78
1.4-1.410.271760.24753106X-RAY DIFFRACTION100
1.41-1.430.27971580.23673086X-RAY DIFFRACTION99.91
1.43-1.450.23371690.21663095X-RAY DIFFRACTION99.94
1.45-1.470.22631680.20453130X-RAY DIFFRACTION99.94
1.47-1.490.21551540.19093102X-RAY DIFFRACTION100
1.49-1.510.18951510.18093092X-RAY DIFFRACTION99.91
1.51-1.530.17751660.1753096X-RAY DIFFRACTION99.88
1.53-1.550.19991530.17333121X-RAY DIFFRACTION100
1.55-1.580.16581530.16833116X-RAY DIFFRACTION99.91
1.58-1.610.20091600.1713112X-RAY DIFFRACTION100
1.61-1.640.18491510.16493157X-RAY DIFFRACTION100
1.64-1.670.19291680.16843084X-RAY DIFFRACTION100
1.67-1.70.1931880.15783107X-RAY DIFFRACTION99.97
1.7-1.740.18391370.15763124X-RAY DIFFRACTION99.94
1.74-1.780.16371480.14293144X-RAY DIFFRACTION100
1.78-1.820.17441760.14793102X-RAY DIFFRACTION99.97
1.82-1.870.16791530.14813155X-RAY DIFFRACTION100
1.87-1.930.18171810.14353109X-RAY DIFFRACTION100
1.93-1.990.1671500.15013149X-RAY DIFFRACTION100
1.99-2.060.18531580.1513167X-RAY DIFFRACTION100
2.06-2.140.1561510.1433142X-RAY DIFFRACTION100
2.14-2.240.12811590.13283129X-RAY DIFFRACTION100
2.24-2.360.15661460.12983189X-RAY DIFFRACTION100
2.36-2.510.14431500.13383177X-RAY DIFFRACTION100
2.51-2.70.17141630.13693174X-RAY DIFFRACTION99.94
2.7-2.970.18521820.14783170X-RAY DIFFRACTION100
2.97-3.40.19091710.14863193X-RAY DIFFRACTION99.97
3.4-4.290.14181630.13573262X-RAY DIFFRACTION100
4.29-51.060.16331970.15313365X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 15.3270247399 Å / Origin y: 45.1534219368 Å / Origin z: 82.6401864379 Å
111213212223313233
T0.13281272297 Å2-0.00111190342475 Å2-0.0056765897343 Å2-0.267976148448 Å2-0.0039062831831 Å2--0.0629111727452 Å2
L0.673477753663 °20.158833270391 °2-0.249393297035 °2-1.05619779216 °2-0.233900225416 °2--0.91455840349 °2
S-0.0486856126003 Å °0.0107693195436 Å °-0.00332018313767 Å °-0.00889408642077 Å °0.0295222656067 Å °-0.0274089217291 Å °0.0206723951804 Å °0.0773589248193 Å °0.0139111504359 Å °
Refinement TLS groupSelection details: all

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