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

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Basic information

Entry
Database: PDB / ID: 7qke
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with inhibitor (surface entropy reduction mutant)
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / P450 / CYP / Tuberculosis / cholesterol / inhibitor / complex / surface / entropy / reduction / 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
Chem-E1V / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSnee, M. / Tunnicliffe, R. / Leys, D. / Levy, C. / Katariya, M.
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
DepositionDec 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4683
Polymers46,4891
Non-polymers9792
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-25 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.010, 119.523, 145.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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: 46489.078 Da / Num. of mol.: 1 / Mutation: K153A, K332A, K333A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / 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-E1V / ethyl 1-(cyclohexylmethyl)-5-pyridin-4-yl-indole-2-carboxylate


Mass: 362.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.53 Å3/Da / Density % sol: 51.38 % / Description: Plate like, very thin
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 22% PEG8000, 0.1M sodium cacodylate pH 5.0, 0.2M sodium acetate trihydrate
Temp details: 4C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→49.22 Å / Num. obs: 21451 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 47.66 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.046 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.202 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2058 / CC1/2: 0.924 / Rpim(I) all: 0.355 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IW0

3iw0


Resolution: 2.3→37.7 Å / SU ML: 0.3126 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2263 1109 5.19 %
Rwork0.1912 20242 -
obs0.1931 21351 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 70 114 3395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283401
X-RAY DIFFRACTIONf_angle_d0.56974636
X-RAY DIFFRACTIONf_chiral_restr0.0379473
X-RAY DIFFRACTIONf_plane_restr0.0037617
X-RAY DIFFRACTIONf_dihedral_angle_d11.4697467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.31691290.32332480X-RAY DIFFRACTION99.58
2.4-2.530.36241500.26942491X-RAY DIFFRACTION99.36
2.53-2.690.25191230.24052507X-RAY DIFFRACTION99.7
2.69-2.90.25351360.2342498X-RAY DIFFRACTION99.77
2.9-3.190.25161350.22112520X-RAY DIFFRACTION99.81
3.19-3.650.23381320.20242532X-RAY DIFFRACTION99.51
3.65-4.60.20661530.15662554X-RAY DIFFRACTION100
4.6-37.70.19281510.15722660X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 6.64673395583 Å / Origin y: 20.1590852159 Å / Origin z: 17.9485208234 Å
111213212223313233
T0.330244879562 Å20.0412151555041 Å20.000589522012228 Å2-0.46148376775 Å2-0.0299315855081 Å2--0.346861128407 Å2
L0.695912654416 °2-0.00234085076341 °20.240231545057 °2-1.28086275279 °2-0.197740537153 °2--1.87428833804 °2
S0.0774421714168 Å °0.00847951264442 Å °-0.0717641197006 Å °-0.00720020158278 Å °-0.0200643806238 Å °0.0066746105643 Å °0.197164920685 Å °0.131262290181 Å °-0.0497927828586 Å °
Refinement TLS groupSelection details: all

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