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

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Basic information

Entry
Database: PDB / ID: 4bfu
TitleCrystal structure of Mycobacterium tuberculosis PanK in complex with a triazole inhibitory compound (1c) and phosphate
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
PHOSPHATE ION / Chem-ZVU / Pantothenate kinase / Pantothenate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 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
B: PANTOTHENATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1346
Polymers73,0672
Non-polymers1,0674
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-47.3 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.600, 150.690, 63.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PANTOTHENATE KINASE / PANTOTHENIC ACID KINASE


Mass: 36533.727 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZVU / N-[1-(5-{[(4-fluorophenyl)methyl]sulfanyl}-4-methyl-4H-1,2,4-triazol-3-yl)ethyl]-2-(trifluoromethyl)benzamide


Mass: 438.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18F4N4OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.96 Å3/Da / Density % sol: 58.43 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 1.8 M SODIUM/POTASSIUM PHOSPHATE, PH 8.2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→60 Å / Num. obs: 39320 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3

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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 4BFS

4bfs


Resolution: 2.28→57.46 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.957 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26328 1972 5 %RANDOM
Rwork0.21889 ---
obs0.22113 37299 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.214 Å2
Baniso -1Baniso -2Baniso -3
1--3.87 Å20 Å20 Å2
2---0.63 Å20 Å2
3---4.5 Å2
Refinement stepCycle: LAST / Resolution: 2.28→57.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4942 0 70 136 5148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195134
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9746992
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0315610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27322.063252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.46815830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.911562
X-RAY DIFFRACTIONr_chiral_restr0.1030.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213970
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_it3.1934.5772446
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.0366.853054
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0785.0142687
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: 2.275→2.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 144 -
Rwork0.314 2697 -
obs--98.61 %

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