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

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Basic information

Entry
Database: PDB / ID: 5ibd
TitleCrystal structure Mycobacterium tuberculosis CYP121 in complex with inhibitor fragment 24a
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-GGJ / PROTOPORPHYRIN IX CONTAINING FE / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 1.2May 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)44,7598
Polymers43,3061
Non-polymers1,4537
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-99 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.890, 77.890, 264.030
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-624-

HOH

21A-634-

HOH

31A-880-

HOH

41A-885-

HOH

51A-888-

HOH

61A-1010-

HOH

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Components

#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
#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-GGJ / 4-(3'-amino[1,1'-biphenyl]-3-yl)-3-(4-methoxyphenyl)-1H-pyrazol-5-amine


Mass: 356.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→44.005 Å / Num. obs: 47127 / % possible obs: 99.55 % / Redundancy: 21.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1359 / Net I/σ(I): 16.33
Reflection shellResolution: 1.77→1.833 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.6159 / Mean I/σ(I) obs: 3.6 / % possible all: 96.16

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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: 1.77→44.005 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.26
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 2281 4.89 %RANDOM
Rwork0.1463 ---
obs0.1483 46639 98.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.77→44.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 95 515 3641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013251
X-RAY DIFFRACTIONf_angle_d1.2564457
X-RAY DIFFRACTIONf_dihedral_angle_d13.5621225
X-RAY DIFFRACTIONf_chiral_restr0.05500
X-RAY DIFFRACTIONf_plane_restr0.007577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80850.22931350.17852503X-RAY DIFFRACTION91
1.8085-1.85060.20441370.17842589X-RAY DIFFRACTION95
1.8506-1.89690.22721490.18022655X-RAY DIFFRACTION97
1.8969-1.94820.20541360.16052727X-RAY DIFFRACTION98
1.9482-2.00550.1911190.15052733X-RAY DIFFRACTION99
2.0055-2.07020.16731410.14522724X-RAY DIFFRACTION99
2.0702-2.14420.20031460.13662750X-RAY DIFFRACTION99
2.1442-2.23010.17311470.13462756X-RAY DIFFRACTION99
2.2301-2.33150.16271290.1332772X-RAY DIFFRACTION99
2.3315-2.45450.17551380.13162800X-RAY DIFFRACTION100
2.4545-2.60820.17521600.13832777X-RAY DIFFRACTION100
2.6082-2.80960.19251320.14772828X-RAY DIFFRACTION100
2.8096-3.09220.1731440.15972838X-RAY DIFFRACTION100
3.0922-3.53950.19271430.15132878X-RAY DIFFRACTION100
3.5395-4.45880.18141600.12882896X-RAY DIFFRACTION100
4.4588-44.01860.19761650.15263132X-RAY DIFFRACTION100

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