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- PDB-4bfs: Crystal structure of Mycobacterium tuberculosis PanK in complex w... -

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Basic information

Entry
Database: PDB / ID: 4bfs
TitleCrystal structure of Mycobacterium tuberculosis PanK in complex with a triazole inhibitory compound (1a)
ComponentsPANTOTHENATE KINASE
KeywordsTRANSFERASE / COA PATHWAY / INHIBITOR
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZVS / Pantothenate kinase / Pantothenate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBjorkelid, C. / Bergfors, T. / Jones, T.A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Biochemical Characterization of Compounds Inhibiting Mycobacterium Tuberculosis Pank
Authors: Bjorkelid, C. / Bergfors, T. / Raichurkar, A.K.V. / Mukherjee, K. / Krishnan, M. / Bandodkar, B. / Jones, T.A.
History
DepositionMar 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PANTOTHENATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0022
Polymers36,5341
Non-polymers4681
Water23413
1
A: PANTOTHENATE KINASE
hetero molecules

A: PANTOTHENATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0044
Polymers73,0672
Non-polymers9372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3970 Å2
ΔGint-28.6 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.280, 105.280, 90.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PANTOTHENATE KINASE / PANTOTHENIC ACID KINASE


Mass: 36533.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase
#2: Chemical ChemComp-ZVS / N-[1-(5-{[2-(4-FLUOROPHENOXY)ETHYL]SULFANYL}-4-METHYL-4H-1,2,4-TRIAZOL-3-YL)ETHYL]-2-(TRIFLUOROMETHYL)BENZAMIDE


Mass: 468.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20F4N4O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.07 Å3/Da / Density % sol: 69.83 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 14.4% (W/V) PEG 8000, 20% (V/V) GLYCEROL, 0.08 M SODIUM CACODYLATE, PH 6.5, AND 0.16 M CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04123
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04123 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 13018 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GEV

2gev


Resolution: 2.9→28.74 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.64 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.589 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24488 639 4.9 %RANDOM
Rwork0.19675 ---
obs0.19914 12375 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.855 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å21.17 Å20 Å2
2--1.17 Å20 Å2
3----3.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 32 13 2484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192531
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9753444
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6695300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75321.87123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.03615411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5151531
X-RAY DIFFRACTIONr_chiral_restr0.10.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211953
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1025.2311206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.9267.8291504
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9155.6771324
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.509 46 -
Rwork0.309 875 -
obs--99.14 %

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