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- PDB-5ibe: Crystal structure Mycobacterium tuberculosis CYP121 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5ibe
TitleCrystal structure Mycobacterium tuberculosis CYP121 in complex with inhibitor fragment 25a
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / Mycobacterium tuberculosis / CYP121 / Fragment based inhibitor screening
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 / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-69M / PROTOPORPHYRIN IX CONTAINING FE / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.624 Å
AuthorsLevy, C.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors.
Authors: Kavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C.W. / Marino, L.B. / de Carvalho, L.P. / Chan, D.S. / Hudson, S.A. / Surade, S. / Leys, D. / Munro, A.W. / Abell, C.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,9409
Polymers43,3061
Non-polymers1,6348
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-93 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.275, 77.275, 263.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-888-

HOH

31A-912-

HOH

41A-1036-

HOH

51A-1038-

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 (bacteria) / Gene: cyp121, MT2336 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPP6, UniProt: P9WPP7*PLUS, EC: 1.14.21.9

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Non-polymers , 5 types, 551 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-69M / 4-[5-amino-4-(3'-amino[1,1'-biphenyl]-3-yl)-1H-pyrazol-3-yl]phenol


Mass: 342.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N4O
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.5-2.1 M ammonium sulfate and 0.1 M sodium MES or Cacodylate from pH 5.5-6.15
PH range: 5.5 - 6.15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.624→46.982 Å / Num. obs: 111039 / % possible obs: 99.77 % / Redundancy: 26 % / CC1/2: 0.99 / Rmerge(I) obs: 0.08826 / Net I/σ(I): 20.35

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHOUSE

Resolution: 1.624→46.982 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.34
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 3682 3.32 %RANDOM
Rwork0.1598 ---
obs0.1605 111039 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.624→46.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 106 543 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043271
X-RAY DIFFRACTIONf_angle_d1.0344480
X-RAY DIFFRACTIONf_dihedral_angle_d12.9571232
X-RAY DIFFRACTIONf_chiral_restr0.034500
X-RAY DIFFRACTIONf_plane_restr0.005579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6237-1.6450.34841300.27533930X-RAY DIFFRACTION93
1.645-1.66760.24951400.25754085X-RAY DIFFRACTION100
1.6676-1.69140.26931460.24624147X-RAY DIFFRACTION100
1.6914-1.71670.30171390.21964177X-RAY DIFFRACTION100
1.7167-1.74350.22661380.20944073X-RAY DIFFRACTION100
1.7435-1.77210.24071440.19034132X-RAY DIFFRACTION100
1.7721-1.80260.23841440.18494187X-RAY DIFFRACTION100
1.8026-1.83540.17921450.18574135X-RAY DIFFRACTION100
1.8354-1.87070.21831370.17844117X-RAY DIFFRACTION100
1.8707-1.90890.20141420.17364162X-RAY DIFFRACTION100
1.9089-1.95040.17821430.1714106X-RAY DIFFRACTION100
1.9504-1.99580.21641400.16974138X-RAY DIFFRACTION100
1.9958-2.04570.19631450.16624141X-RAY DIFFRACTION100
2.0457-2.1010.16641440.16984133X-RAY DIFFRACTION100
2.101-2.16280.18361490.1584138X-RAY DIFFRACTION100
2.1628-2.23260.22971400.1544148X-RAY DIFFRACTION100
2.2326-2.31240.20121350.14924152X-RAY DIFFRACTION100
2.3124-2.4050.15711390.15134162X-RAY DIFFRACTION100
2.405-2.51440.15921480.14934095X-RAY DIFFRACTION100
2.5144-2.6470.19431410.15424151X-RAY DIFFRACTION100
2.647-2.81280.17421460.15264123X-RAY DIFFRACTION100
2.8128-3.030.16471430.15864143X-RAY DIFFRACTION100
3.03-3.33480.17211380.1594167X-RAY DIFFRACTION100
3.3348-3.81720.15831430.13924127X-RAY DIFFRACTION100
3.8172-4.80850.14981410.12694155X-RAY DIFFRACTION100
4.8085-47.0020.16571420.16074133X-RAY DIFFRACTION100

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