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

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Basic information

Entry
Database: PDB / ID: 7zqr
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / P450 / monooxygenase / cholesterol / mycobacterium / inhibitor / tuberculosis / CYP125
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 / 4-(4-methoxyphenyl)pyridine / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSnee, M. / Katariya, M. / Tunnicliffe, R. / 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 2, 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

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)143,56525
Polymers139,9903
Non-polymers3,57522
Water13,241735
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,21514
Polymers46,6631
Non-polymers1,55113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6936
Polymers46,6631
Non-polymers1,0295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6575
Polymers46,6631
Non-polymers9944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.782, 69.109, 144.785
Angle α, β, γ (deg.)90.000, 94.008, 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)
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 , 6 types, 757 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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-JK9 / 4-(4-methoxyphenyl)pyridine


Mass: 185.222 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H11NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
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: 1.79→68.22 Å / Num. obs: 126949 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 8.9
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6281 / CC1/2: 0.513 / Rpim(I) all: 0.454 / Rrim(I) all: 0.816

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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: 1.79→68.22 Å / SU ML: 0.2055 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.4292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2083 6421 5.06 %
Rwork0.1799 120470 -
obs0.1813 126891 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.55 Å2
Refinement stepCycle: LAST / Resolution: 1.79→68.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9661 0 228 735 10624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008210342
X-RAY DIFFRACTIONf_angle_d0.902914112
X-RAY DIFFRACTIONf_chiral_restr0.05711446
X-RAY DIFFRACTIONf_plane_restr0.00831867
X-RAY DIFFRACTIONf_dihedral_angle_d9.12151418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.810.3062070.26663976X-RAY DIFFRACTION99.52
1.81-1.830.31752140.25114000X-RAY DIFFRACTION99.69
1.83-1.850.26462060.24064002X-RAY DIFFRACTION99.79
1.85-1.880.26221930.22994003X-RAY DIFFRACTION99.83
1.88-1.90.27872220.2313957X-RAY DIFFRACTION99.74
1.9-1.930.26532270.23964000X-RAY DIFFRACTION99.58
1.93-1.960.29232320.25663958X-RAY DIFFRACTION99.81
1.96-1.980.2752170.22713988X-RAY DIFFRACTION99.88
1.98-2.020.25512340.21894000X-RAY DIFFRACTION99.95
2.02-2.050.26272350.21693941X-RAY DIFFRACTION99.98
2.05-2.080.25722030.20554029X-RAY DIFFRACTION99.83
2.08-2.120.23752230.19823977X-RAY DIFFRACTION99.83
2.12-2.160.2241960.19214021X-RAY DIFFRACTION99.67
2.16-2.210.2282100.18623996X-RAY DIFFRACTION99.88
2.21-2.260.21692360.19284027X-RAY DIFFRACTION99.93
2.26-2.310.22442130.1873965X-RAY DIFFRACTION99.93
2.31-2.370.21892120.19224021X-RAY DIFFRACTION99.95
2.37-2.430.24062110.19464002X-RAY DIFFRACTION99.98
2.43-2.50.21122160.18344014X-RAY DIFFRACTION99.93
2.5-2.580.22242350.1854011X-RAY DIFFRACTION99.93
2.58-2.670.22752020.1864018X-RAY DIFFRACTION99.95
2.67-2.780.22051930.19434042X-RAY DIFFRACTION99.88
2.78-2.910.23111880.1894061X-RAY DIFFRACTION99.98
2.91-3.060.23212300.19924005X-RAY DIFFRACTION99.95
3.06-3.250.2281820.19824058X-RAY DIFFRACTION99.91
3.25-3.50.20722290.1744032X-RAY DIFFRACTION99.95
3.5-3.860.17072090.16324043X-RAY DIFFRACTION99.81
3.86-4.410.16182100.13964068X-RAY DIFFRACTION99.93
4.41-5.560.17052140.14324073X-RAY DIFFRACTION99.7
5.56-68.220.16472220.15944182X-RAY DIFFRACTION99.84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8946082009620.069842895961-0.1956014454071.63740957310.1700441049370.9600093937490.0089749797218-0.000674944528029-0.0225477378779-0.043326920074-0.03217965680680.0527971594340.0491989523114-0.03534124598720.02323965398140.1108580965040.00775657092903-0.02462141092260.1698223573310.004041498188470.19965741109313.83329251824.1570639378768.286213961
21.1576366155-0.060853118958-0.4252102051521.67110469796-0.2810696657171.42509614807-0.00108925880804-0.263603859078-0.0265430137210.0194745354607-0.0511517400064-0.310904315624-0.0111426801310.5918655731510.03769079274930.2514918294170.0248165500047-0.00551591240890.4823433113680.001599707036370.22770747649150.8894329267-0.27342708430535.9190817454
31.23390270112-0.506360971896-0.1255039024270.754338482241-0.2847132768531.52627439287-0.0841711883474-0.0426080537471-0.0547298290556-0.1890627386660.07261320329450.1013017410590.315456150091-0.1750288032160.006343793978550.506150038405-0.06110948743230.02894805203060.219673478015-0.03594769898350.27776607699225.9608227565-18.38930256737.7227207306
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 18 through 1201)AA - B18 - 12011
22(chain 'B' and resid 19 through 427)BD19 - 4271 - 405
33(chain 'C' and resid 19 through 430)CF19 - 4301 - 412

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