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- PDB-7qwn: Crystal structure of CYP125 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 7qwn
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / tuberculosis / mycobacterium / inhibitor / cholesterol / p450 / cytochrome / TB / monooxygenase / CYP125
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / biological process involved in interaction with host / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
ethyl 5-pyridin-4-yl-1~{H}-indole-2-carboxylate / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSnee, M. / Katariya, M. / Levy, C. / Leys, D.
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
DepositionJan 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
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
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
B: Steroid C26-monooxygenase
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,80728
Polymers139,5763
Non-polymers4,23125
Water16,628923
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.052, 69.203, 144.540
Angle α, β, γ (deg.)90.000, 94.389, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-994-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Steroid C26-monooxygenase / Cholest-4-en-3-one 26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25S)-3-oxocholest-4-en- ...Cholest-4-en-3-one 26-monooxygenase / Cholest-4-en-3-one C26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / Cholesterol C26-monooxygenase / Cholesterol C26-monooxygenase [(25S)-3beta-hydroxycholest-5-en-26-oate forming] / Cytochrome P450 125 / Steroid C27-monooxygenase


Mass: 46525.238 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp125, cyp125A1, Rv3545c, MTCY03C7.11 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P9WPP1, cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming]

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Non-polymers , 5 types, 948 molecules

#2: Chemical ChemComp-DQE / ethyl 5-pyridin-4-yl-1~{H}-indole-2-carboxylate


Mass: 266.295 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 2.45 Å3/Da / Density % sol: 49.76 % / Description: Irregular rock-like
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 1.9 M Ammonium sulphate, 0.1 M MES, pH 6.2 / PH range: 6-6.5 / 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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.93→68.33 Å / Num. obs: 101498 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.08 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.056 / Rrim(I) all: 0.103 / Net I/σ(I): 5.9
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5012 / CC1/2: 0.505 / Rpim(I) all: 0.602 / Rrim(I) all: 1.088 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XN8

2xn8


Resolution: 1.93→68.33 Å / SU ML: 0.2672 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.8283
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 5220 5.15 %
Rwork0.1805 96167 -
obs0.1825 101387 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.97 Å2
Refinement stepCycle: LAST / Resolution: 1.93→68.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9633 0 266 923 10822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005110378
X-RAY DIFFRACTIONf_angle_d0.742314178
X-RAY DIFFRACTIONf_chiral_restr0.04341441
X-RAY DIFFRACTIONf_plane_restr0.00691875
X-RAY DIFFRACTIONf_dihedral_angle_d8.79631420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.41681690.38513110X-RAY DIFFRACTION99.3
1.95-1.970.3621720.3373258X-RAY DIFFRACTION99.59
1.97-20.38311890.30353100X-RAY DIFFRACTION99.7
2-2.020.28561900.26893213X-RAY DIFFRACTION99.59
2.02-2.050.29141570.25143168X-RAY DIFFRACTION99.85
2.05-2.080.25691750.23143202X-RAY DIFFRACTION99.59
2.08-2.110.25291810.22163176X-RAY DIFFRACTION99.67
2.11-2.140.24431590.21033205X-RAY DIFFRACTION99.79
2.14-2.170.27581880.21123162X-RAY DIFFRACTION99.64
2.17-2.210.23391390.20013205X-RAY DIFFRACTION99.73
2.21-2.250.23961660.2013229X-RAY DIFFRACTION99.94
2.25-2.290.26851740.20333168X-RAY DIFFRACTION99.76
2.29-2.330.21911760.19733198X-RAY DIFFRACTION99.59
2.33-2.380.25081770.20833171X-RAY DIFFRACTION99.73
2.38-2.430.27631640.21383195X-RAY DIFFRACTION99.67
2.43-2.490.2541660.1973241X-RAY DIFFRACTION99.71
2.49-2.550.22411540.19273211X-RAY DIFFRACTION99.91
2.55-2.620.23191690.18643176X-RAY DIFFRACTION99.91
2.62-2.70.24621710.18983216X-RAY DIFFRACTION99.88
2.7-2.780.2221770.18053222X-RAY DIFFRACTION99.97
2.78-2.880.2141880.18343187X-RAY DIFFRACTION99.97
2.88-30.261720.19643234X-RAY DIFFRACTION99.94
3-3.130.25281630.20443220X-RAY DIFFRACTION99.94
3.13-3.30.21851820.18623213X-RAY DIFFRACTION99.79
3.3-3.510.22241850.16313207X-RAY DIFFRACTION99.91
3.51-3.780.18481930.1533190X-RAY DIFFRACTION99.88
3.78-4.160.15761910.13513220X-RAY DIFFRACTION99.82
4.16-4.760.15832020.12693235X-RAY DIFFRACTION99.97
4.76-60.19671640.15963275X-RAY DIFFRACTION99.94
6-68.330.22451670.17973360X-RAY DIFFRACTION99.72
Refinement TLS params.Method: refined / Origin x: 29.5856603153 Å / Origin y: -4.28861869186 Å / Origin z: 38.3623178017 Å
111213212223313233
T0.276083612394 Å20.0450662527231 Å2-0.0628459617955 Å2-0.191960772586 Å20.0210262106699 Å2--0.358375029497 Å2
L0.149977758031 °20.0466145996672 °2-0.277832912492 °2-0.217609279098 °20.0904584270419 °2--1.00699407418 °2
S-0.04735584103 Å °0.0128482481373 Å °-0.0285102303213 Å °-0.126846693203 Å °0.00150192847163 Å °-0.0330424101958 Å °0.134526327976 Å °0.125202748387 Å °0.0554915704269 Å °
Refinement TLS groupSelection details: all

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