SAXSdb — 1ekq

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

HYDROXYETHYLTHIAZOLE KINASE

Bacillus subtilis

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)	No other associated polymer	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
2	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)	No other associated polymer	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

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 1EKQ	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 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）	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
1EKK CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN THE R3 FORM WITH HYDROXYETHYLTHIAZOLE 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)	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
1EKK CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN THE R3 FORM WITH HYDROXYETHYLTHIAZOLE Deposited 2000-03-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–272（272 aa）	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
1EKK CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN THE R3 FORM WITH HYDROXYETHYLTHIAZOLE Deposited 2000-03-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 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)	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
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 6 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ekq
Deposition date deposition_date	2000-03-09
Structure title title	CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN R3 SPACE GROUP
Keywords keywords	Alpha-beta, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	35.12 Å
Radius of gyration Rg (electron density) rg_electron	34.83 Å
Forward intensity I(0) i0	43723100.00
Molecular weight molecular_weight	52934.0 kDa
Excluded volume excluded_volume	66363 Å³
Envelope volume envelope_volume	88760 Å³
Hydration-shell volume shell_volume	20982 Å³
Envelope diameter envelope_diameter	111.3 Å
Shell Rg shell_rg	41.98 Å
Envelope Rg envelope_rg	33.70 Å
Shape Rg shape_rg	34.83 Å
Total Rg total_rg	35.35 Å
Total atoms total_atoms	3716
Residues n_residues	507
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	111.9 Å
Rg (real space) rg_real	35.41 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	4.3720e+07
I(0) uncertainty (real space) i0_real_error	7.0130e+05
Rg (reciprocal space) rg_reciprocal	35.24 Å
I(0) (reciprocal space) i0_reciprocal	43720000.0000
Solution quality estimate total_estimate	0.6511
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.252
Kurtosis Kurtosis kurtosis	-1.162
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11580000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.124; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.300; Smooth: 0.787

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ekqa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.2 — Thiamin biosynthesis kinases

Domain ID domain_id	d1ekqb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.2 — Thiamin biosynthesis kinases

CATH v4.4 (2 domains)

Domain ID domain_id	1ekqA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	1ekqB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

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8. Citations (1)

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Unit-cell length a length_a	77.500 Å
Unit-cell length b length_b	77.500 Å
Unit-cell length c length_c	230.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2510

Description description	HYDROXYETHYLTHIAZOLE KINASE
Molecular weight formula_weight	28272.2 kDa
EC 编号 ec_number	2.7.1.50
Mutation mutation	C198(CSD)
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3974

CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN R3 SPACE GROUP

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

HYDROXYETHYLTHIAZOLE KINASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	258

fit	/app/data/saxs_computation/ek/1ekq/1ekq.fit
pddf	/app/data/pr_computation/ek/1ekq/1ekq.pr.out
profile	/app/data/saxs_computation/ek/1ekq/1ekq.dat