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- PDB-2gev: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -

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Basic information

Entry
Database: PDB / ID: 2gev
TitlePantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with a coenzyme A derivative, Form-II (LT)
ComponentsPantothenate kinase
KeywordsTRANSFERASE / HOMODIMER / COA BIOSYNTHESIS / NUCLEOTIDE BINDING
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-COK / Pantothenate kinase / Pantothenate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDas, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / 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.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / 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.
History
DepositionMar 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)37,2999
Polymers35,7811
Non-polymers1,5188
Water5,152286
1
A: Pantothenate kinase
hetero molecules

A: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,59918
Polymers71,5622
Non-polymers3,03716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area10020 Å2
ΔGint-37 kcal/mol
Surface area26550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.388, 104.388, 90.594
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-702-

HOH

DetailsThe following symmetry operation will generate the second subunit of the homodimeric MtPanK molecule: Symmetry:Y, X, -Z; TransSymm: 556

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Components

#1: Protein Pantothenate kinase / / PANK / Pantothenic acid kinase


Mass: 35780.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: coaA(Rv1092c) / Plasmid: PET-28a(+) (NOVAGEN) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase
#2: Chemical ChemComp-COK / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-4-{[3-({2-[(2-HYDROXYETHYL)DITHIO]ETHYL}AMINO)-3-OXOPROPYL]AMINO}-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE / S-(THIOETHYLHYDROXY)COENZYME A


Mass: 843.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H40N7O17P3S2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.9 Å3/Da / Density % sol: 68.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-15%(w/v) PEG8000, 0.05M NaCl, 0.05-0.1M NaOAc in 0.1M Na-Cacodylate buffer of pH 6.5, 0.001M Beta-mercaptoethanol was present in the protein buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 3, 2005
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→28.64 Å / Num. obs: 24164 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 25.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 10 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2374 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
MAR345345DTBdata collection
CCP4(TRUNCATE)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1ESM

1esm


Resolution: 2.35→28.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1252803.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MLF FUNCTION THROUGHOUT THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1170 4.8 %RANDOM
Rwork0.213 ---
obs0.213 24137 99.7 %-
all-24137 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.7104 Å2 / ksol: 0.321857 e/Å3
Displacement parametersBiso mean: 57.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.48 Å28.62 Å20 Å2
2--8.48 Å20 Å2
3----16.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.35→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 96 286 2864
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 2.35→2.43 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.328 102 4.3 %
Rwork0.336 2265 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep+cme.paramprotein+cme.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4DRGCNS_COA_2ME+GLY+TRIS.Param

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