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- PDB-1ekq: CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN R3 SPACE GROUP -

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Basic information

Entry
Database: PDB / ID: 1ekq
TitleCRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN R3 SPACE GROUP
ComponentsHYDROXYETHYLTHIAZOLE KINASE
KeywordsTRANSFERASE / Alpha-beta
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: 1.5 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 1.3Feb 15, 2012Group: Derived calculations
Revision 1.4Nov 12, 2014Group: Non-polymer description
Revision 1.5Nov 20, 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
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

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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


Theoretical massNumber of molelcules
Total (without water)56,5442
Polymers56,5442
Non-polymers00
Water4,648258
1
A: HYDROXYETHYLTHIAZOLE KINASE

A: HYDROXYETHYLTHIAZOLE KINASE

A: HYDROXYETHYLTHIAZOLE KINASE


Theoretical massNumber of molelcules
Total (without water)84,8163
Polymers84,8163
Non-polymers00
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 area5230 Å2
ΔGint-27 kcal/mol
Surface area26760 Å2
MethodPISA
2
B: HYDROXYETHYLTHIAZOLE KINASE

B: HYDROXYETHYLTHIAZOLE KINASE

B: HYDROXYETHYLTHIAZOLE KINASE


Theoretical massNumber of molelcules
Total (without water)84,8163
Polymers84,8163
Non-polymers00
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
Buried area5280 Å2
ΔGint-27 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.5, 77.5, 230.4
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

21A-342-

HOH

31B-351-

HOH

41B-398-

HOH

DetailsBiological assembly is a trimer. The crystallographic three-fold generates two trimers 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris, 100mM ammonium sulfate, 30% PEG4000, 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: A1 / Wavelength: 0.914
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 14, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 83000 / Num. obs: 73978 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.158 / % possible all: 55
Reflection
*PLUS
Num. measured all: 264643
Reflection shell
*PLUS
% possible obs: 55 % / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.5→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3437 -Random
Rwork0.216 ---
all-69857 --
obs-67629 82 %-
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 0 258 3974
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d23.34
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.34
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.291

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