← Back to search
1ekk

CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN THE R3 FORM WITH HYDROXYETHYLTHIAZOLE

Method: X-RAY DIFFRACTION Dmax: 112.3 Å Quality: REASONABLE
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

HYDROXYETHYLTHIAZOLE KINASE

Bacillus subtilis

UniProt P39593

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–272 Mutation：C198(CSD) Non-standard monomer：Yes (specific site not provided by mmCIF) TZE 2-(4-METHYL-THIAZOL-5-YL)-ETHANOL × 3 SO2 SULFUR DIOXIDE × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM Tris, 100mM ammonium sulfate, 30% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.242
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–272 Mutation：C198(CSD) Non-standard monomer：Yes (specific site not provided by mmCIF) TZE 2-(4-METHYL-THIAZOL-5-YL)-ETHANOL × 1 SO2 SULFUR DIOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM Tris, 100mM ammonium sulfate, 30% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.242
3 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–272 Mutation：C198(CSD) Non-standard monomer：Yes (specific site not provided by mmCIF) TZE 2-(4-METHYL-THIAZOL-5-YL)-ETHANOL × 3 SO2 SULFUR DIOXIDE × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM Tris, 100mM ammonium sulfate, 30% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.242

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1EKK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C3Q CRYSTAL STRUCTURE OF NATIVE THIAZOLE KINASE IN THE MONOCLINIC FORM Deposited 1999-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–272（272 aa）
Chain B 1–272（272 aa）
Chain C 1–272（272 aa）
Not recorded CL CHLORIDE ION × 1 TZE 2-(4-METHYL-THIAZOL-5-YL)-ETHANOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.6；100 MM TRIS, 20 % (W/V) PEG 8000, pH 8.60
Resolution 2.00 Å R-free 0.242
1EKQ CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN R3 SPACE GROUP Deposited 2000-03-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–272（272 aa）
Mutation：C198(CSD) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM Tris, 100mM ammonium sulfate, 30% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.251
1EKQ CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN R3 SPACE GROUP Deposited 2000-03-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–272（272 aa）
Mutation：C198(CSD) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM Tris, 100mM ammonium sulfate, 30% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.251
1ESJ CRYSTAL STRUCTURE OF THIAZOLE KINASE MUTANT (C198S) Deposited 2000-04-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–272（272 aa）
Chain B 1–272（272 aa）
Chain C 1–272（272 aa）
Mutation：C198S Mutation：C198S Mutation：C198S SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；21% peg4k, 0.1M ammonium sulfate, 0.1 tris.HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Resolution 1.80 Å R-free 0.253
1ESQ CRYSTAL STRUCTURE OF THIAZOLE KINASE MUTANT (C198S) WITH ATP AND THIAZOLE PHOSPHATE. Deposited 2000-04-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–272（272 aa）
Chain B 1–272（272 aa）
Chain C 1–272（272 aa）
Mutation：C198S Mutation：C198S Mutation：C198S MG MAGNESIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 TZP 4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；21%PEG4K, 0.1M Ammonium sulfate, 0.1M Tris. HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Resolution 2.50 Å R-free 0.282

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIM_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–272； UniProt 1–272 Author chain B； PDBConstruct 1–272； UniProt 1–272

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1ekk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ekk
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1ekk
Deposition date deposition_date2000-03-09
Structure title titleCRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN THE R3 FORM WITH HYDROXYETHYLTHIAZOLE
Keywords keywordsAlpha-beta, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.53 Å
Radius of gyration Rg (electron density) rg_electron35.26 Å
Forward intensity I(0) i049672900.00
Molecular weight molecular_weight56284.0 kDa
Excluded volume excluded_volume70467 ų
Envelope volume envelope_volume95789 ų
Hydration-shell volume shell_volume22448 ų
Envelope diameter envelope_diameter113.3 Å
Shell Rg shell_rg42.15 Å
Envelope Rg envelope_rg34.13 Å
Shape Rg shape_rg35.26 Å
Total Rg total_rg35.75 Å
Total atoms total_atoms3948
Residues n_residues536
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.3 Å
Rg (real space) rg_real35.83 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real4.9670e+07
I(0) uncertainty (real space) i0_real_error7.9300e+05
Rg (reciprocal space) rg_reciprocal35.65 Å
I(0) (reciprocal space) i0_reciprocal49660000.0000
Solution quality estimate total_estimate0.6616
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary25.0 Å
Skewness Skewness skewness0.269
Kurtosis Kurtosis kurtosis-1.131
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18370000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.172; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.368; Smooth: 0.713
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ekka_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.72 — Ribokinase-like
Superfamily Superfamily superfamilyc.72.1 — Ribokinase-like
Family Family familyc.72.1.2 — Thiamin biosynthesis kinases
Domain ID domain_idd1ekkb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.72 — Ribokinase-like
Superfamily Superfamily superfamilyc.72.1 — Ribokinase-like
Family Family familyc.72.1.2 — Thiamin biosynthesis kinases

CATH v4.4 (2 domains)

Domain ID domain_id1ekkA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily20 — Ribokinase
Domain ID domain_id1ekkB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily20 — Ribokinase
▶

8. Citations (1)

▶

9. Files and Curves (10)