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

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Basic information

Entry
Database: PDB / ID: 7nqo
TitleMycobacterium tuberculosis Cytochrome P450 CYP121 in complex with lead compound 21
ComponentsMycocyclosin synthase
KeywordsMETAL BINDING PROTEIN / Mycobacterium tuberculosis / heme-binding / inhibitor / complex
Function / homology
Function and homology information


mycocyclosin synthase / cyclase activity / 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 / carbon monoxide binding / monooxygenase activity / 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 / Chem-ULZ / 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

Downloads & links

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Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,71617
Polymers43,3061
Non-polymers2,41016
Water12,755708
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-135 kcal/mol
Surface area16910 Å2
Unit cell
Length a, b, c (Å)77.924, 77.924, 264.042
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-599-

HOH

21A-959-

HOH

31A-983-

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 , 7 types, 724 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ULZ / 4-[4-[2-(5-bromanyl-1~{H}-indol-3-yl)ethyl]pyrimidin-2-yl]morpholine


Mass: 387.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19BrN4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.6 Å3/Da / Density % sol: 52.8 %
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: 1.59961→65.3823 Å / Num. obs: 63724 / % possible obs: 100 % / Redundancy: 18.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.041 / Rrim(I) all: 0.175 / Net I/σ(I): 7.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 18 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 6252 / CC1/2: 0.913 / Rpim(I) all: 0.174 / Rrim(I) all: 0.747 / % possible all: 100

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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→65.38 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 2000 3.14 %
Rwork0.167 61724 -
obs0.1681 63724 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.98 Å2 / Biso mean: 23.9947 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 1.6→65.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 223 709 3963
Biso mean--29.96 33.01 -
Num. residues----394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.640.25891390.25742974436
1.64-1.680.29221400.240543174457
1.68-1.730.27871410.220943544495
1.73-1.790.28531390.202642854424
1.79-1.850.2521410.192643664507
1.85-1.930.25781410.20943384479
1.93-2.020.21921400.189543304470
2.02-2.120.23331420.194643714513
2.12-2.250.21911420.172443814523
2.25-2.430.19941430.15544224565
2.43-2.670.18511440.151544284572
2.67-3.060.17531440.155544594603
3.06-3.850.1721480.137645414689
3.86-65.380.18691560.156748354991

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