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- PDB-7nqm: Mycobacterium tuberculosis Cytochrome P450 CYP121 in complex with... -

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Basic information

Entry
Database: PDB / ID: 7nqm
TitleMycobacterium tuberculosis Cytochrome P450 CYP121 in complex with lead compound 10
ComponentsMycocyclosin synthase
KeywordsMETAL BINDING PROTEIN / Mycobacterium tuberculosis / Heme-binding / Inhibitor / Complex
Function / homology
Function and homology information


mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
HEME C / 3-(2-pyrimidin-4-ylethyl)-1~{H}-indole / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSelvam, I.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)DTP CASE BB/R505870/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R009775/1 United Kingdom
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: A new strategy for hit generation: Novel in cellulo active inhibitors of CYP121A1 from Mycobacterium tuberculosis via a combined X-ray crystallographic and phenotypic screening approach (XP screen).
Authors: Frederickson, M. / Selvam, I.R. / Evangelopoulos, D. / McLean, K.J. / Katariya, M.M. / Tunnicliffe, R.B. / Campbell, B. / Kavanagh, M.E. / Charoensutthivarakul, S. / Blankley, R.T. / Levy, C. ...Authors: Frederickson, M. / Selvam, I.R. / Evangelopoulos, D. / McLean, K.J. / Katariya, M.M. / Tunnicliffe, R.B. / Campbell, B. / Kavanagh, M.E. / Charoensutthivarakul, S. / Blankley, R.T. / Levy, C.W. / de Carvalho, L.P.S. / Leys, D. / Munro, A.W. / Coyne, A.G. / Abell, C.
History
DepositionMar 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,50124
Polymers43,3061
Non-polymers3,19523
Water12,070670
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-210 kcal/mol
Surface area17150 Å2
Unit cell
Length a, b, c (Å)76.626, 76.626, 261.788
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-647-

HOH

21A-1028-

HOH

31A-1071-

HOH

41A-1150-

HOH

51A-1162-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mycocyclosin synthase / Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43305.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: cyp121, Rv2276, MTCY339.34c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP7, mycocyclosin synthase

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Non-polymers , 6 types, 693 molecules

#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-UMZ / 3-(2-pyrimidin-4-ylethyl)-1~{H}-indole


Mass: 223.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 50.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 3.5 M Ammonium Sulphate, 1 M MES / PH range: 5-6.5

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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: Dec 11, 2018
RadiationMonochromator: Single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.59819→66.3605 Å / Num. obs: 60608 / % possible obs: 98.84 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.022 / Rrim(I) all: 0.094 / Net I/σ(I): 15.3
Reflection shellResolution: 1.59819→1.66 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5826 / CC1/2: 0.918 / Rpim(I) all: 0.194 / Rrim(I) all: 0.854 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n40

1n40


Resolution: 1.6→66.36 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 2000 3.3 %
Rwork0.1639 58608 -
obs0.1648 60608 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.52 Å2 / Biso mean: 22.9122 Å2 / Biso min: 8.71 Å2
Refinement stepCycle: final / Resolution: 1.6→66.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 314 675 4027
Biso mean--32.62 32.65 -
Num. residues----395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.30461370.28734018415597
1.64-1.680.26691390.23414043418298
1.68-1.730.23661390.21114102424198
1.73-1.790.23161400.19014082422298
1.79-1.850.21841380.18414070420898
1.85-1.930.21071410.18034132427399
1.93-2.010.2411420.18914149429199
2.01-2.120.2261400.1594130427099
2.12-2.250.17831440.14484197434199
2.25-2.430.20181430.14934170431399
2.43-2.670.1671430.15424230437399
2.67-3.060.17611470.157942854432100
3.06-3.850.15431480.141843544502100
3.85-66.360.16981590.16146464805100

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