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- PDB-5xmb: Mycobacterium tuberculosis Pantothenate kinase mutant F247A -

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Basic information

Entry
Database: PDB / ID: 5xmb
TitleMycobacterium tuberculosis Pantothenate kinase mutant F247A
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: 3.2 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 13, 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
C: Pantothenate kinase
D: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8998
Polymers142,5154
Non-polymers3844
Water59433
1
A: Pantothenate kinase
B: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4504
Polymers71,2582
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-67 kcal/mol
Surface area26070 Å2
2
C: Pantothenate kinase
D: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4504
Polymers71,2582
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-51 kcal/mol
Surface area25500 Å2
Unit cell
Length a, b, c (Å)84.829, 104.719, 145.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A5 - 22
2111B5 - 22
1211A42 - 79
2211B42 - 79
1311A88 - 242
2311B88 - 242
1411A258 - 312
2411B258 - 312
1121C9 - 18
2121D9 - 18
1221C43 - 78
2221D43 - 78
1321C86 - 247
2321D86 - 247
1421C269 - 311
2421D269 - 311

NCS ensembles :
ID
2
1

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.996482, -0.082722, -0.013422), (-0.075601, 0.818241, 0.569883), (-0.036159, 0.568893, -0.821617)-25.78837, -4.26479, 10.00869

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Components

#1: Protein
Pantothenate kinase / Pantothenic acid kinase


Mass: 35628.754 Da / Num. of mol.: 4 / Mutation: F247A
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPA7, pantothenate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.5
Details: 25%PEG 3350, 200mM Ammonium sulphate, 100mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953725 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 3.2→84.96 Å / Num. obs: 20268 / % possible obs: 89.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.249 / Net I/σ(I): 4.4
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2961 / % possible all: 93.9

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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: 3.2→84.96 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.71 / SU B: 49.442 / SU ML: 0.839 / Cross valid method: THROUGHOUT / ESU R Free: 0.795 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35941 1032 5.2 %RANDOM
Rwork0.29135 ---
obs0.29497 18786 90.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.349 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å2-0 Å2-0 Å2
2--8.84 Å2-0 Å2
3----5.27 Å2
Refinement stepCycle: 1 / Resolution: 3.2→84.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 20 33 8073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198207
X-RAY DIFFRACTIONr_bond_other_d0.0130.027738
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.96411214
X-RAY DIFFRACTIONr_angle_other_deg1.082317546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24251054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05122.28329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.066151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4881575
X-RAY DIFFRACTIONr_chiral_restr0.0650.21335
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219325
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021904
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 64 -
Rwork0.38 1286 -
obs--84.85 %

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