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

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Basic information

Entry
Database: PDB / ID: 7zxd
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-KB9 / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 20, 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)143,66514
Polymers139,9903
Non-polymers3,67511
Water6,720373
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3558
Polymers46,6631
Non-polymers1,6917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6553
Polymers46,6631
Non-polymers9922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6553
Polymers46,6631
Non-polymers9922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.237, 69.218, 144.140
Angle α, β, γ (deg.)90.000, 94.350, 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
Components on special symmetry positions
IDModelComponents
11A-799-

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: 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]

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Non-polymers , 5 types, 384 molecules

#2: Chemical
ChemComp-KB9 / 1-[1-(2-piperidin-4-ylethyl)-5-pyridin-4-yl-indol-2-yl]butan-1-one


Mass: 375.507 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C24H29N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1M MES pH 6.2, 1.9M 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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.09→47.91 Å / Num. obs: 79538 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Net I/σ(I): 19.5
Reflection shellResolution: 2.09→2.13 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4496 / CC1/2: 0.904 / Rpim(I) all: 0.2 / % possible all: 99.2

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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: 2.09→47.91 Å / SU ML: 0.2543 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 3938 4.95 %
Rwork0.196 75575 -
obs0.1971 79513 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.69 Å2
Refinement stepCycle: LAST / Resolution: 2.09→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9650 0 257 373 10280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002610303
X-RAY DIFFRACTIONf_angle_d0.572214050
X-RAY DIFFRACTIONf_chiral_restr0.03931430
X-RAY DIFFRACTIONf_plane_restr0.00461863
X-RAY DIFFRACTIONf_dihedral_angle_d10.79431435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.34121410.27042643X-RAY DIFFRACTION99.11
2.12-2.140.32651380.25862728X-RAY DIFFRACTION99.14
2.14-2.170.30371250.24272622X-RAY DIFFRACTION97.65
2.17-2.20.31041630.2372668X-RAY DIFFRACTION99.75
2.2-2.230.24431170.232660X-RAY DIFFRACTION97.71
2.23-2.260.22751480.22522704X-RAY DIFFRACTION99.93
2.26-2.30.29241080.22562697X-RAY DIFFRACTION98.42
2.3-2.340.26161460.22042653X-RAY DIFFRACTION99.36
2.34-2.380.22581480.23142664X-RAY DIFFRACTION98.77
2.38-2.420.27031290.22432687X-RAY DIFFRACTION99.4
2.42-2.470.2731370.23822686X-RAY DIFFRACTION98.81
2.47-2.520.31131340.23382687X-RAY DIFFRACTION99.68
2.52-2.570.25641240.23132718X-RAY DIFFRACTION98.71
2.57-2.630.25211550.23182692X-RAY DIFFRACTION99.96
2.63-2.70.26151190.22632669X-RAY DIFFRACTION98.9
2.7-2.770.24551360.22112713X-RAY DIFFRACTION99.13
2.77-2.850.24881620.21742697X-RAY DIFFRACTION100
2.85-2.950.27681510.22682702X-RAY DIFFRACTION99.3
2.95-3.050.24781480.22862665X-RAY DIFFRACTION99.4
3.05-3.170.26591640.22842691X-RAY DIFFRACTION99.51
3.17-3.320.24311410.21192714X-RAY DIFFRACTION99.72
3.32-3.490.21520.19642713X-RAY DIFFRACTION99.76
3.49-3.710.20761360.17972707X-RAY DIFFRACTION99.82
3.71-40.18741600.16632721X-RAY DIFFRACTION99.86
4-4.40.16621250.14952729X-RAY DIFFRACTION99.93
4.4-5.040.17811610.1522737X-RAY DIFFRACTION99.93
5.04-6.340.18561440.18452773X-RAY DIFFRACTION99.93
6.34-47.910.16241260.16522835X-RAY DIFFRACTION99.2
Refinement TLS params.Method: refined / Origin x: 29.8258885146 Å / Origin y: -4.3654008365 Å / Origin z: 38.1678568254 Å
111213212223313233
T0.429381280476 Å20.0741839597022 Å20.0146598155003 Å2-0.359895852161 Å20.0164035909175 Å2--0.349356560263 Å2
L0.196829204037 °20.0509339574195 °2-0.307265659992 °2-0.217190785418 °20.106766968004 °2--1.15957753491 °2
S-0.058667513871 Å °0.115281214199 Å °-0.0224622008427 Å °-0.229574249563 Å °0.0193593592669 Å °-0.0799969526099 Å °0.216114318798 Å °0.173164126755 Å °0.0408450786566 Å °
Refinement TLS groupSelection details: all

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