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- PDB-5xlv: Mycobacterium tuberculosis Pantothenate kinase mutant F254A -

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Basic information

Entry
Database: PDB / ID: 5xlv
TitleMycobacterium tuberculosis Pantothenate kinase mutant F254A
ComponentsPantothenate kinase
KeywordsTRANSFERASE / Homodimer / CoA biosynthesis / Nucleotide binding / Concerted movement / Structural transformation
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
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPaul, A. / Kumar, P. / Surolia, A. / Vijayan, M.
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Biochemical and structural studies of mutants indicate concerted movement of the dimer interface and ligand-binding region of Mycobacterium tuberculosis pantothenate kinase
Authors: Paul, A. / Kumar, P. / Surolia, A. / Vijayan, M.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2005
Title: Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis.
Authors: Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2006
Title: Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK.
Authors: Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M.
#3: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009
Title: Mycobacterium tuberculosis pantothenate kinase: possible changes in location of ligands during enzyme action.
Authors: Chetnani, B. / Das, S. / Kumar, P. / Surolia, A. / Vijayan, M.
#4: Journal: J. Mol. Biol. / Year: 2010
Title: M. tuberculosis pantothenate kinase: dual substrate specificity and unusual changes in ligand locations.
Authors: Chetnani, B. / Kumar, P. / Surolia, A. / Vijayan, M.
#5: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2011
Title: Location and conformation of pantothenate and its derivatives in Mycobacterium tuberculosis pantothenate kinase: insights into enzyme action.
Authors: Chetnani, B. / Kumar, P. / Abhinav, K.V. / Chhibber, M. / Surolia, A. / Vijayan, M.
History
DepositionMay 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Pantothenate kinase
B: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,66549
Polymers71,2582
Non-polymers3,40847
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-10 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.820, 120.820, 125.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

21A-640-

HOH

31A-693-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pantothenate kinase / Pantothenic acid kinase


Mass: 35628.754 Da / Num. of mol.: 2 / Mutation: F254A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: coaA, Rv1092c, MTV017.45c / Plasmid: PET-28A(+) / Details (production host): Novagen / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P9WPA7, pantothenate kinase

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Non-polymers , 5 types, 674 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 3.86 Å3/Da / Density % sol: 68.16 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: 10-15% PEG 400, 1.25M Ammonium sulphate, 100mM HEPES sodium salt

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→24.58 Å / Num. obs: 97939 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14187 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GEU

2geu


Resolution: 1.8→24.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.324 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21259 4891 5 %RANDOM
Rwork0.17754 ---
obs0.17928 93034 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å2-0 Å2
2---0.2 Å2-0 Å2
3---0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.8→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 216 627 5604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9836865
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06722.134239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71615814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3891560
X-RAY DIFFRACTIONr_chiral_restr0.1680.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213808
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_it2.2772.1272401
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1963.1723004
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9142.6432699
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.1320.2278625
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 355 -
Rwork0.291 6806 -
obs--99.8 %

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