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- PDB-1esq: CRYSTAL STRUCTURE OF THIAZOLE KINASE MUTANT (C198S) WITH ATP AND ... -

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Basic information

Entry
Database: PDB / ID: 1esq
TitleCRYSTAL STRUCTURE OF THIAZOLE KINASE MUTANT (C198S) WITH ATP AND THIAZOLE PHOSPHATE.
ComponentsHYDROXYETHYLTHIAZOLE KINASE
KeywordsTRANSFERASE / trimer / alpha-beta protein
Function / homologyHydroxyethylthiazole kinase / Ribokinase-like / Hydroxyethylthiazole kinase family / hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding / Hydroxyethylthiazole kinase
Function and homology information
Specimen sourceBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.5 Å resolution
AuthorsCampobasso, N. / Mathews, I.I. / Begley, T.P. / Ealick, S.E.
Citation
Journal: Biochemistry / Year: 2000
Title: Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
Authors: Campobasso, N. / Mathews, I.I. / Begley, T.P. / Ealick, S.E.
#1: Journal: Arch.Microbiol. / Year: 1999
Title: Thiamin Biosynthesis in Prokaryotes.
Authors: Begley, T.P. / Downs, D. / Ealick, S. / McLafferty, F. / Van Loon, D. / Taylor, S. / Campobasso, N. / Chiu, H.J. / Kinsland, C. / Reddick, J.J. / Xi, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 10, 2000 / Release: Aug 9, 2000
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 9, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jan 31, 2018Structure modelExperimental preparationexptl_crystal_grow_exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROXYETHYLTHIAZOLE KINASE
B: HYDROXYETHYLTHIAZOLE KINASE
C: HYDROXYETHYLTHIAZOLE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,32216
Polyers88,8893
Non-polymers2,43313
Water3,225179
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)10710
ΔGint (kcal/M)-103
Surface area (Å2)26540
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)54.08, 100.84, 72.51
Angle α, β, γ (deg.)90, 95.1, 90
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 1 types, 3 molecules ABC

#1: Protein/peptide HYDROXYETHYLTHIAZOLE KINASE / / THZ KINASE


Mass: 29629.633 Da / Num. of mol.: 3 / Details: N-TERMINAL HIS TAG / Mutation: C198S / Source: (gene. exp.) Bacillus subtilis (bacteria) / Genus: Bacillus / Plasmid name: PQE30 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P39593, hydroxyethylthiazole kinase

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Non-polymers , 5 types, 192 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Chemical ChemComp-TZP / 4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE


Mass: 223.187 Da / Num. of mol.: 3 / Formula: C6H10NO4PS
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Formula: H2O / Water

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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: 2.21 / Density percent sol: 44.47 %
Crystal growTemp: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 21%PEG4K, 0.1M Ammonium sulfate, 0.1M Tris. HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal
*PLUS
Density percent sol: 44 %
Crystal grow
*PLUS
pH: 8.6 / Method: vapor diffusion, sitting drop
Details: drop consists of equal volume of protein and reservoir solutions
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
130 mg/mlprotein1drop
20.05 mMThz1drop
30.05 mMATP1drop
40.1 mM1dropMgCl2
5100 mMTris-HCl1reservoir
620 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 19-ID / Synchrotron site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: APS / Detector: CCD / Collection date: Jun 18, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 37.3 Å2 / D resolution high: 2.5 Å / D resolution low: 2 Å / Number all: 26976 / Number obs: 26796 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.068 / NetI over sigmaI: 7.9 / Redundancy: 4.1 % / Percent possible obs: 99.9
Reflection shellRmerge I obs: 0.258 / Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / Number unique all: 2710 / Redundancy: 4 % / Percent possible all: 1
Reflection
*PLUS
Number measured all: 111367
Reflection shell
*PLUS
Percent possible obs: 1 / MeanI over sigI obs: 4.3

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefineR Free selection details: random / Sigma F: 1 / Sigma I: 0.5 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.282 / R factor R work: 0.209 / R factor all: 0.212 / R factor obs: 0.211 / Highest resolution: 2.5 Å / Lowest resolution: 2 Å / Number reflection R free: 1300 / Number reflection all: 26793 / Number reflection obs: 26790 / Percent reflection obs: 94.9
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 5739 / Nucleic acid: 0 / Ligand: 143 / Solvent: 179 / Total: 6061
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d1.229
X-RAY DIFFRACTIONc_improper_angle_d21.59
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d

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