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- PDB-1esj: CRYSTAL STRUCTURE OF THIAZOLE KINASE MUTANT (C198S) -

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Basic information

Entry
Database: PDB / ID: 1esj
TitleCRYSTAL STRUCTURE OF THIAZOLE KINASE MUTANT (C198S)
ComponentsHYDROXYETHYLTHIAZOLE KINASE
KeywordsTRANSFERASE / trimer / alpha-beta protein
Function / homology
Function and homology information


hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydroxyethylthiazole kinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
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.
History
DepositionApr 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_residues ...database_2 / pdbx_unobs_or_zero_occ_residues / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)89,0815
Polymers88,8893
Non-polymers1922
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-56 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.06, 100.89, 73.07
Angle α, β, γ (deg.)90, 96.02, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYDROXYETHYLTHIAZOLE KINASE / THZ KINASE


Mass: 29629.633 Da / Num. of mol.: 3 / Mutation: C198S
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL HIS TAG / Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P39593, hydroxyethylthiazole kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 21% peg4k, 0.1M ammonium sulfate, 0.1 tris.HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal
*PLUS
Density % 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
IDConc.Common 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 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorDetector: CCD / Date: Jun 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 83184 / Num. obs: 83184 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.375 / Num. unique all: 7921 / % possible all: 93.6
Reflection
*PLUS
Num. measured all: 340088
Reflection shell
*PLUS
% possible obs: 93.6 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.8→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3200 -random
Rwork0.229 ---
all0.231 73829 --
obs0.23 62186 89.84 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6240 0 10 342 6592
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.187
X-RAY DIFFRACTIONc_dihedral_angle_d21.91
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.229 / Rfactor Rwork: 0.231

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