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- PDB-1ekk: CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN THE R3 FORM W... -

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Basic information

Entry
Database: PDB / ID: 1ekk
TitleCRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN THE R3 FORM WITH HYDROXYETHYLTHIAZOLE
ComponentsHYDROXYETHYLTHIAZOLE KINASE
KeywordsTRANSFERASE / Alpha-beta
Function / homology
Function and homology information


hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine diphosphate biosynthetic process / thiamine 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
SULFUR DIOXIDE / 2-(4-METHYL-THIAZOL-5-YL)-ETHANOL / Hydroxyethylthiazole kinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsCampobasso, N. / Mathews, I.I. / Begley, T.P. / Ealick, S.E.
CitationJournal: 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
DepositionMar 9, 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: Derived calculations / Version format compliance
Revision 1.3Nov 12, 2014Group: Non-polymer description
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,9596
Polymers56,5442
Non-polymers4154
Water3,279182
1
A: HYDROXYETHYLTHIAZOLE KINASE
hetero molecules

A: HYDROXYETHYLTHIAZOLE KINASE
hetero molecules

A: HYDROXYETHYLTHIAZOLE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4389
Polymers84,8163
Non-polymers6226
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6350 Å2
ΔGint-39 kcal/mol
Surface area28780 Å2
MethodPISA, PQS
2
B: HYDROXYETHYLTHIAZOLE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4793
Polymers28,2721
Non-polymers2072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: HYDROXYETHYLTHIAZOLE KINASE
hetero molecules

B: HYDROXYETHYLTHIAZOLE KINASE
hetero molecules

B: HYDROXYETHYLTHIAZOLE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4389
Polymers84,8163
Non-polymers6226
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.040, 78.040, 232.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-301-

SO2

21A-301-

SO2

31B-302-

SO2

41B-302-

SO2

Detailsbiological assembly is a trimer. The crystallographic three-fold generates a trimer from chain A and chain B, respectively

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Components

#1: Protein HYDROXYETHYLTHIAZOLE KINASE


Mass: 28272.166 Da / Num. of mol.: 2 / Mutation: C198(CSD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P39593, hydroxyethylthiazole kinase
#2: Chemical ChemComp-TZE / 2-(4-METHYL-THIAZOL-5-YL)-ETHANOL / 4-METHYL-5-HYDROXYETHYLTHIAZOLE


Mass: 143.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NOS
#3: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris, 100mM ammonium sulfate, 30% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
2100 mMTris-HCl1reservoir
3100 mMammonium sulfate1reservoir
430 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.94
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 35800 / Num. obs: 35426 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.98 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.172 / % possible all: 99
Reflection
*PLUS
Num. measured all: 209109
Reflection shell
*PLUS
% possible obs: 99 % / Mean I/σ(I) obs: 8.7

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1752 -Random
Rwork0.205 ---
all0.207 35444 --
obs0.207 35372 99 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 24 182 4130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d22.04
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.04
LS refinement shell
*PLUS
Rfactor Rfree: 0.209 / Rfactor Rwork: 0.22

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