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- PDB-7zt0: Crystal structure of CYP125 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 7zt0
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / p450 / Cytochrome / CYP125 / cholesterol / tuberculosis / mycobacterium / inhibitor / monooxygenase
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 / Chem-JUR / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,88115
Polymers93,3272
Non-polymers2,55413
Water5,386299
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9288
Polymers46,6631
Non-polymers1,2647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9537
Polymers46,6631
Non-polymers1,2906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.808, 90.096, 152.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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, 312 molecules

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


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


Mass: 349.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.99→90.1 Å / Num. obs: 65089 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 43.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Net I/σ(I): 11.4
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.474 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4531 / CC1/2: 0.627 / Rpim(I) all: 0.603 / % possible all: 100

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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: 1.99→76.44 Å / SU ML: 0.2564 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.3829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2365 3221 4.96 %
Rwork0.2046 61760 -
obs0.2062 64981 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.62 Å2
Refinement stepCycle: LAST / Resolution: 1.99→76.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6434 0 167 299 6900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326871
X-RAY DIFFRACTIONf_angle_d0.63259371
X-RAY DIFFRACTIONf_chiral_restr0.0409953
X-RAY DIFFRACTIONf_plane_restr0.00481239
X-RAY DIFFRACTIONf_dihedral_angle_d9.5149950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.34031450.31562635X-RAY DIFFRACTION99.86
2.02-2.050.31811440.30512662X-RAY DIFFRACTION99.86
2.05-2.080.30261240.2852630X-RAY DIFFRACTION99.93
2.08-2.120.34041140.28832687X-RAY DIFFRACTION100
2.12-2.160.3131610.27542627X-RAY DIFFRACTION99.93
2.16-2.20.27931220.27262666X-RAY DIFFRACTION99.86
2.2-2.250.35151490.25132643X-RAY DIFFRACTION100
2.25-2.290.30071360.24952656X-RAY DIFFRACTION100
2.29-2.350.25581390.2362687X-RAY DIFFRACTION99.96
2.35-2.410.26211280.24262646X-RAY DIFFRACTION99.96
2.41-2.470.2631460.2312651X-RAY DIFFRACTION100
2.47-2.540.22171320.22362672X-RAY DIFFRACTION99.96
2.54-2.630.23651400.23942689X-RAY DIFFRACTION99.93
2.63-2.720.29131430.24672669X-RAY DIFFRACTION100
2.72-2.830.24591480.26042677X-RAY DIFFRACTION100
2.83-2.960.27721430.23752681X-RAY DIFFRACTION100
2.96-3.110.27561160.22882704X-RAY DIFFRACTION100
3.11-3.310.27811300.2322686X-RAY DIFFRACTION100
3.31-3.570.25791450.20032716X-RAY DIFFRACTION100
3.57-3.920.22111710.18312688X-RAY DIFFRACTION100
3.92-4.490.18351660.15842713X-RAY DIFFRACTION100
4.49-5.660.19991300.15952786X-RAY DIFFRACTION100
5.66-76.440.19391490.17362889X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: -15.8225939328 Å / Origin y: -10.2372165231 Å / Origin z: 18.7436541256 Å
111213212223313233
T0.326527521923 Å20.0168618996558 Å2-0.0121017678557 Å2-0.315449453274 Å2-0.0279003104148 Å2--0.378243607014 Å2
L0.681639207861 °20.0736928874031 °20.590124265811 °2-0.556829504322 °20.39457301681 °2--1.4295019003 °2
S-0.047071904338 Å °-0.0369842355876 Å °0.0670340938236 Å °0.0265969004952 Å °-0.0288249185783 Å °0.0128515214085 Å °-0.163861677103 Å °-0.096286974707 Å °0.0684753269273 Å °
Refinement TLS groupSelection details: all

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