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- PDB-1c3q: CRYSTAL STRUCTURE OF NATIVE THIAZOLE KINASE IN THE MONOCLINIC FORM -

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Basic information

Entry
Database: PDB / ID: 1c3q
TitleCRYSTAL STRUCTURE OF NATIVE THIAZOLE KINASE IN THE MONOCLINIC FORM
ComponentsHydroxyethylthiazole kinase
KeywordsTRANSFERASE / ALPHA-BETA / ATP BINDING / KINASE
Function / homology
Function and homology information


hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / phosphorylation / 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
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
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 1, 2016Group: Source and taxonomy
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Hydroxyethylthiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4027
Polymers88,9373
Non-polymers4654
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-38 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.920, 101.180, 73.330
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hydroxyethylthiazole kinase / / THZ KINASE


Mass: 29645.695 Da / Num. of mol.: 3
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TZE / 2-(4-METHYL-THIAZOL-5-YL)-ETHANOL / 4-METHYL-5-HYDROXYETHYLTHIAZOLE


Mass: 143.207 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H9NOS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growpH: 8.6 / Details: 100 MM TRIS, 20 % (W/V) PEG 8000, pH 8.60
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
Temperature: 18 ℃ / 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: CHESS / Beamline: F1 / Wavelength: 0.922
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 2→36.5 Å / Num. obs: 220523 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / % possible all: 85.4
Reflection
*PLUS
Num. obs: 51102 / Num. measured all: 162565
Reflection shell
*PLUS
% possible obs: 95 % / Mean I/σ(I) obs: 5.8

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2→20 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
Details: USED TORSION ANGLE, SIMULATED ANNEALING WITH MAXIMUM LIKELIHOOD TARGET.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2467 -RANDOM
Rwork0.206 ---
obs0.206 51052 93.7 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6240 0 28 207 6475
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.18
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.251 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.269 / Rfactor Rwork: 0.28

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