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

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Basic information

Entry
Database: PDB / ID: 7zic
TitleCrystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
ComponentsSteroid C26-monooxygenase
KeywordsOXIDOREDUCTASE / CYP / CYP125 / P450 / Cholesterol / oxidase / inhibitor / complex / Cytochrome / tuberculosis / MTB / Mycobacterium / 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
Chem-5YG / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSnee, M. / Levy, C. / Kavanagh, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: J.Med.Chem. / Year: 2025
Title: Fragment-Based Development of Small Molecule Inhibitors Targeting Mycobacterium tuberculosis Cholesterol Metabolism.
Authors: Kavanagh, M.E. / McLean, K.J. / Gilbert, S.H. / Amadi, C.N. / Snee, M. / Tunnicliffe, R.B. / Arora, K. / Boshoff, H.I.M. / Fanourakis, A. / Rebollo-Lopez, M.J. / Ortega, F. / Levy, C.W. / ...Authors: Kavanagh, M.E. / McLean, K.J. / Gilbert, S.H. / Amadi, C.N. / Snee, M. / Tunnicliffe, R.B. / Arora, K. / Boshoff, H.I.M. / Fanourakis, A. / Rebollo-Lopez, M.J. / Ortega, F. / Levy, C.W. / Munro, A.W. / Leys, D. / Abell, C. / Coyne, A.G.
History
DepositionApr 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 30, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)144,45328
Polymers139,9903
Non-polymers4,46325
Water12,052669
1
A: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0969
Polymers46,6631
Non-polymers1,4338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0658
Polymers46,6631
Non-polymers1,4017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid C26-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,29211
Polymers46,6631
Non-polymers1,62910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.233, 68.684, 144.472
Angle α, β, γ (deg.)90.000, 93.968, 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 / Mutation: None
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: pET21 / 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, 694 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-5YG / ~{N}-[(4-methoxyphenyl)methyl]-4-(pyridin-4-ylmethyl)aniline


Mass: 304.386 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H20N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.93 % / Description: rough "boulder like" chunks
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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.9→144.13 Å / Num. obs: 104289 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5050 / CC1/2: 0.518 / Rpim(I) all: 0.731 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XN8

2xn8


Resolution: 1.9→72.06 Å / SU ML: 0.2507 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2236 5021 4.82 %
Rwork0.1875 99160 -
obs0.1892 104181 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→72.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9637 0 286 669 10592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006910606
X-RAY DIFFRACTIONf_angle_d0.800914507
X-RAY DIFFRACTIONf_chiral_restr0.04751477
X-RAY DIFFRACTIONf_plane_restr0.00811914
X-RAY DIFFRACTIONf_dihedral_angle_d9.41821484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.39681750.33723201X-RAY DIFFRACTION98.68
1.92-1.940.33631730.31123256X-RAY DIFFRACTION98.51
1.94-1.970.31832060.29373223X-RAY DIFFRACTION98.53
1.97-1.990.29711660.26023277X-RAY DIFFRACTION98.6
1.99-2.020.30221670.24183258X-RAY DIFFRACTION98.5
2.02-2.050.25761550.2413241X-RAY DIFFRACTION98.32
2.05-2.080.25831690.2323282X-RAY DIFFRACTION98.29
2.08-2.110.26761490.22573245X-RAY DIFFRACTION98.21
2.11-2.140.26981550.22443283X-RAY DIFFRACTION98.06
2.14-2.170.26311690.21743283X-RAY DIFFRACTION98.97
2.17-2.210.25181640.20863285X-RAY DIFFRACTION99.19
2.21-2.250.24721830.21083301X-RAY DIFFRACTION99.26
2.25-2.30.25121510.21543293X-RAY DIFFRACTION99.34
2.3-2.340.25161780.2143270X-RAY DIFFRACTION99.34
2.34-2.390.25351560.20333344X-RAY DIFFRACTION99.4
2.39-2.450.28481810.20173315X-RAY DIFFRACTION99.43
2.45-2.510.23541770.1943236X-RAY DIFFRACTION99.33
2.51-2.580.24291780.18783322X-RAY DIFFRACTION99.54
2.58-2.650.2831580.17933355X-RAY DIFFRACTION99.57
2.65-2.740.24631660.18843308X-RAY DIFFRACTION99.46
2.74-2.840.24071820.19443308X-RAY DIFFRACTION99.69
2.84-2.950.24841550.21083330X-RAY DIFFRACTION99.63
2.95-3.090.22781480.19753337X-RAY DIFFRACTION99.74
3.09-3.250.25081450.19663352X-RAY DIFFRACTION99.63
3.25-3.450.22621620.17933375X-RAY DIFFRACTION99.86
3.45-3.720.19421590.16983316X-RAY DIFFRACTION99.86
3.72-4.090.17451610.15243377X-RAY DIFFRACTION99.89
4.09-4.690.16051550.13733378X-RAY DIFFRACTION99.72
4.69-5.90.19351850.16613375X-RAY DIFFRACTION99.72
5.9-72.060.21930.18623434X-RAY DIFFRACTION99.45
Refinement TLS params.Method: refined / Origin x: 29.5663890974 Å / Origin y: -4.40434136692 Å / Origin z: 38.1904031996 Å
111213212223313233
T0.280614694514 Å20.0342674365441 Å2-0.0208196264411 Å2-0.193895973628 Å20.0273931427792 Å2--0.318283014464 Å2
L0.214188862879 °2-0.048259190521 °2-0.52169330302 °2-0.324400795283 °20.248429468039 °2--1.63578495854 °2
S-0.0715970221382 Å °-0.0139741227738 Å °-0.0440927217371 Å °-0.146683485786 Å °0.00828931789604 Å °-0.0405639919793 Å °0.182146961557 Å °0.140376920689 Å °0.0631536194858 Å °
Refinement TLS groupSelection details: all

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