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- PDB-7r1i: Crystal structure of CYP125 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 7r1i
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / 125 / tuberculosis / inhibitor / cholesterol / oxidase / CYP125 / P450 / Cytochrome
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-HIH / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 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

Downloads & links

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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)143,80516
Polymers139,9903
Non-polymers3,81513
Water5,981332
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3588
Polymers46,6631
Non-polymers1,6957
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6934
Polymers46,6631
Non-polymers1,0293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7534
Polymers46,6631
Non-polymers1,0903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.943, 69.466, 144.901
Angle α, β, γ (deg.)90.000, 94.138, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: 46663.383 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / 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, 345 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-HIH / ethyl 1-(2-piperidin-4-ylethyl)-5-pyridin-4-yl-indole-2-carboxylate


Mass: 377.479 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H27N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 MES pH 5.5-6.7, 1.7M Ammonium / PH range: 5.5-6.7 / 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: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.24→144.52 Å / Num. obs: 66030 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 40.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Net I/σ(I): 8.5
Reflection shellResolution: 2.24→2.29 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4386 / CC1/2: 0.717 / Rpim(I) all: 0.379 / Rrim(I) all: 0.709 / % 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: 2XN8

2xn8


Resolution: 2.24→144.52 Å / SU ML: 0.2697 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2395 3343 5.07 %
Rwork0.2022 62658 -
obs0.2041 66001 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.03 Å2
Refinement stepCycle: LAST / Resolution: 2.24→144.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9617 0 263 332 10212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003410192
X-RAY DIFFRACTIONf_angle_d0.611213876
X-RAY DIFFRACTIONf_chiral_restr0.04061411
X-RAY DIFFRACTIONf_plane_restr0.00461832
X-RAY DIFFRACTIONf_dihedral_angle_d7.90581467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.270.31811360.27912608X-RAY DIFFRACTION99.93
2.27-2.310.34141440.26942588X-RAY DIFFRACTION99.93
2.31-2.340.30961510.26572567X-RAY DIFFRACTION99.82
2.34-2.380.28761290.26912600X-RAY DIFFRACTION100
2.38-2.420.30071410.26362587X-RAY DIFFRACTION99.93
2.42-2.470.30381360.27242605X-RAY DIFFRACTION99.89
2.47-2.510.36521450.25652582X-RAY DIFFRACTION99.96
2.51-2.560.29271390.25852625X-RAY DIFFRACTION99.96
2.56-2.620.34091090.23872556X-RAY DIFFRACTION99.66
2.62-2.680.26451430.23332653X-RAY DIFFRACTION99.89
2.68-2.750.29211260.23652593X-RAY DIFFRACTION99.82
2.75-2.820.28481340.23022571X-RAY DIFFRACTION99.78
2.82-2.910.28541380.24432649X-RAY DIFFRACTION99.93
2.91-30.26881390.25892581X-RAY DIFFRACTION99.96
3-3.110.31151600.25352596X-RAY DIFFRACTION99.93
3.11-3.230.26861390.23452612X-RAY DIFFRACTION100
3.23-3.380.23981560.2112597X-RAY DIFFRACTION99.96
3.38-3.560.22971660.19372575X-RAY DIFFRACTION99.93
3.56-3.780.21171360.18992608X-RAY DIFFRACTION99.78
3.78-4.070.20751290.16922659X-RAY DIFFRACTION99.93
4.07-4.480.20221290.15192615X-RAY DIFFRACTION99.78
4.48-5.130.19131340.15232648X-RAY DIFFRACTION99.89
5.13-6.460.19671580.18212653X-RAY DIFFRACTION100
6.46-144.520.18161260.1642730X-RAY DIFFRACTION99.44
Refinement TLS params.Method: refined / Origin x: 29.9813726626 Å / Origin y: -5.5973934925 Å / Origin z: 38.2481497756 Å
111213212223313233
T0.400920943787 Å20.085734765388 Å2-0.0418576218293 Å2-0.282947457001 Å20.0377584372905 Å2--0.508137854421 Å2
L0.22777441327 °20.0206301535845 °2-0.52743880303 °2-0.224295744595 °20.223192039008 °2--1.78707315153 °2
S-0.0920369612371 Å °-0.00767435639989 Å °-0.0399885560601 Å °-0.159003645334 Å °0.017331369558 Å °-0.0750037847854 Å °0.280945046703 Å °0.220585425942 Å °0.0634773924084 Å °
Refinement TLS groupSelection details: all

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