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

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Basic information

Entry
Database: PDB / ID: 7yxf
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / P450 / cholesterol / tuberculosis / cytochrome / CYP125 / 125A1 / Heme / Iron / Metalloprotein / TB / mycobacterium
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / biological process involved in interaction with host / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 1-(2-piperazin-1-ylethyl)-5-pyridin-4-yl-indole / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_refine_tls / pdbx_refine_tls_group
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)143,33515
Polymers139,9903
Non-polymers3,34512
Water16,268903
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5863
Polymers46,6631
Non-polymers9232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7785
Polymers46,6631
Non-polymers1,1154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9717
Polymers46,6631
Non-polymers1,3076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.445, 69.383, 144.353
Angle α, β, γ (deg.)90.000, 94.289, 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

#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)
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]
#2: Chemical ChemComp-I6Y / 1-(2-piperazin-1-ylethyl)-5-pyridin-4-yl-indole


Mass: 306.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H22N4 / 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.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 903 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 1.7M Ammonium sulphate / 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: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.85→143.95 Å / Num. obs: 114696 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 30.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 9.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5642 / CC1/2: 0.503 / Rpim(I) all: 0.633 / Rrim(I) all: 1.129 / % possible all: 99.6

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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: 1.85→143.95 Å / SU ML: 0.2637 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7808
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2207 5824 5.08 %
Rwork0.1759 108726 -
obs0.1781 114550 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.52 Å2
Refinement stepCycle: LAST / Resolution: 1.85→143.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9630 0 228 903 10761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011810639
X-RAY DIFFRACTIONf_angle_d1.072514551
X-RAY DIFFRACTIONf_chiral_restr0.05861472
X-RAY DIFFRACTIONf_plane_restr0.00991955
X-RAY DIFFRACTIONf_dihedral_angle_d15.37843957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.38692130.36233594X-RAY DIFFRACTION99.22
1.87-1.890.3691850.33553547X-RAY DIFFRACTION99.18
1.89-1.920.332030.30453622X-RAY DIFFRACTION99.27
1.92-1.940.30891740.27673589X-RAY DIFFRACTION99.52
1.94-1.970.2991910.24913608X-RAY DIFFRACTION99.74
1.97-1.990.2771920.23483590X-RAY DIFFRACTION99.71
1.99-2.020.27182100.20783582X-RAY DIFFRACTION99.48
2.02-2.050.24392000.21013622X-RAY DIFFRACTION99.66
2.05-2.080.26552200.20153556X-RAY DIFFRACTION99.95
2.08-2.120.26431870.20413645X-RAY DIFFRACTION99.56
2.12-2.150.24241870.20513587X-RAY DIFFRACTION99.55
2.15-2.190.24521950.19453638X-RAY DIFFRACTION99.77
2.19-2.240.22092080.18973626X-RAY DIFFRACTION99.74
2.24-2.280.23741780.20683560X-RAY DIFFRACTION99.6
2.28-2.330.25722230.20333616X-RAY DIFFRACTION99.82
2.33-2.390.23432030.18843617X-RAY DIFFRACTION99.61
2.39-2.440.26061800.18593601X-RAY DIFFRACTION99.55
2.44-2.510.22341980.1753600X-RAY DIFFRACTION99.76
2.51-2.580.22511940.17513657X-RAY DIFFRACTION99.56
2.58-2.670.22051970.17143623X-RAY DIFFRACTION99.97
2.67-2.760.22631930.17573606X-RAY DIFFRACTION99.5
2.76-2.870.25781580.18573649X-RAY DIFFRACTION99.79
2.87-3.010.25472000.19633634X-RAY DIFFRACTION99.64
3.01-3.160.21421760.18363653X-RAY DIFFRACTION99.51
3.16-3.360.23042000.16863623X-RAY DIFFRACTION99.71
3.36-3.620.19442050.15793646X-RAY DIFFRACTION99.64
3.62-3.990.20292060.14193649X-RAY DIFFRACTION99.92
3.99-4.560.14051940.12243671X-RAY DIFFRACTION99.95
4.56-5.750.18921900.14123696X-RAY DIFFRACTION99.85
5.75-143.950.20881640.17493819X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: 29.5230791777 Å / Origin y: -4.39967057838 Å / Origin z: 38.32483544 Å
111213212223313233
T0.294310273786 Å20.0390899817055 Å2-0.0229851923952 Å2-0.210975190781 Å20.0183088184567 Å2--0.2969068284 Å2
L0.163114256699 °20.00856755855737 °2-0.29844940301 °2-0.164996831903 °20.144980691476 °2--0.977907557221 °2
S-0.0285120805206 Å °0.0276728329041 Å °-0.0264019230422 Å °-0.105488041608 Å °0.00457783289242 Å °-0.0162955463683 Å °0.100113142889 Å °0.100779693431 Å °0.0290893754214 Å °
Refinement TLS groupSelection details: all

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