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

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Basic information

Entry
Database: PDB / ID: 7zsu
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / P450 / cholesterol / monooxygenase / tuberculosis / inhibitor / mycobacterium / cytochrome
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 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / methyl 3-pyridin-4-ylbenzoate / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionMay 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Feb 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)142,98113
Polymers139,9903
Non-polymers2,99110
Water4,990277
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8025
Polymers46,6631
Non-polymers1,1394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5894
Polymers46,6631
Non-polymers9263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5894
Polymers46,6631
Non-polymers9263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.195, 68.896, 144.104
Angle α, β, γ (deg.)90.000, 93.960, 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-JV3 / methyl 3-pyridin-4-ylbenzoate


Mass: 213.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H11NO2 / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 49.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 1.9 M Ammonium sulphate, 0.1 M MES, pH 6.2 / 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: 2.2→63.51 Å / Num. obs: 68265 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 36.36 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.046 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4587 / CC1/2: 0.662 / Rpim(I) all: 0.314 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XN8

2xn8


Resolution: 2.2→60.2 Å / SU ML: 0.2604 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2334 3392 4.98 %
Rwork0.2092 64695 -
obs0.2104 68087 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9588 0 208 277 10073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003210063
X-RAY DIFFRACTIONf_angle_d0.581113693
X-RAY DIFFRACTIONf_chiral_restr0.03871400
X-RAY DIFFRACTIONf_plane_restr0.00491818
X-RAY DIFFRACTIONf_dihedral_angle_d8.16351350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.32051310.32262628X-RAY DIFFRACTION97.39
2.23-2.260.41831210.38462670X-RAY DIFFRACTION97.93
2.26-2.30.2731430.262635X-RAY DIFFRACTION98.65
2.3-2.340.26431520.25122679X-RAY DIFFRACTION99.26
2.34-2.380.29141420.25872655X-RAY DIFFRACTION98.76
2.38-2.420.26851270.25652675X-RAY DIFFRACTION99.26
2.42-2.470.24421590.24852665X-RAY DIFFRACTION99.16
2.47-2.520.30671280.24132665X-RAY DIFFRACTION99.93
2.52-2.570.29031300.23412738X-RAY DIFFRACTION99.76
2.57-2.630.28851470.2322679X-RAY DIFFRACTION99.96
2.63-2.70.28621390.23272676X-RAY DIFFRACTION99.75
2.7-2.770.24441650.23282667X-RAY DIFFRACTION99.72
2.77-2.850.24941550.23942721X-RAY DIFFRACTION99.9
2.85-2.950.25091230.2472722X-RAY DIFFRACTION99.86
2.95-3.050.28351380.25562653X-RAY DIFFRACTION99.79
3.05-3.170.27641550.23912716X-RAY DIFFRACTION99.86
3.17-3.320.21681400.20872704X-RAY DIFFRACTION99.86
3.32-3.490.24131340.20292711X-RAY DIFFRACTION99.96
3.49-3.710.23511470.2012684X-RAY DIFFRACTION99.79
3.71-40.18841410.17922742X-RAY DIFFRACTION99.93
4-4.40.18851500.15712704X-RAY DIFFRACTION100
4.4-5.030.17281290.15612744X-RAY DIFFRACTION99.83
5.04-6.340.22171400.19442756X-RAY DIFFRACTION99.69
6.34-60.20.20021560.18142806X-RAY DIFFRACTION99.5
Refinement TLS params.Method: refined / Origin x: 29.9516558672 Å / Origin y: -4.47689629655 Å / Origin z: 37.9004000848 Å
111213212223313233
T0.356350084127 Å20.0451155284972 Å2-0.014663792026 Å2-0.222169112206 Å20.0204255609534 Å2--0.359841542658 Å2
L0.190044975421 °20.0213098275083 °2-0.327861826806 °2-0.194297222237 °20.160414416954 °2--1.23536920423 °2
S-0.0718957061262 Å °0.0228938269918 Å °-0.0507908789925 Å °-0.175351107896 Å °0.0270246074103 Å °-0.0457961588467 Å °0.206758662816 Å °0.148818930725 Å °0.0551043955614 Å °
Refinement TLS groupSelection details: all

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