SAXSdb — 1bko

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

THYMIDYLATE SYNTHASE A

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–279 Chain B； UniProt 2–279	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.75 Å R-free 0.320
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–279 Chain D； UniProt 2–279	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.75 Å R-free 0.320

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 1BKO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B02 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS Deposited 1998-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–279（279 aa）	Not recorded	UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 1 C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.25；pH 6.25	Resolution 2.50 Å R-free 0.233
1BKP THERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS Deposited 1998-07-09	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–279（278 aa） Chain B 2–279（278 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.70 Å R-free 0.206
1BSF THERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS Deposited 1998-07-10	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–279（278 aa） Chain B 2–279（278 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.301
1BSP THERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS Deposited 1998-07-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–279（278 aa） Chain B 2–279（278 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.260

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

View Construct and Data Evidence

UniProt name	TYSA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–278； UniProt 2–279 Author chain B； PDBConstruct 1–278； UniProt 2–279 Author chain C； PDBConstruct 1–278； UniProt 2–279 Author chain D； PDBConstruct 1–278； UniProt 2–279

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	1bko
Deposition date deposition_date	1998-07-09
Structure title title	THERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS
Keywords keywords	METHYLTRANSFERASE, DTMP SYNTHASE; METHYLTRANSFERASE
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	46.48 Å
Radius of gyration Rg (electron density) rg_electron	46.63 Å
Forward intensity I(0) i0	243968000.00
Molecular weight molecular_weight	130320.0 kDa
Excluded volume excluded_volume	163210 Å³
Envelope volume envelope_volume	224950 Å³
Hydration-shell volume shell_volume	40335 Å³
Envelope diameter envelope_diameter	149.9 Å
Shell Rg shell_rg	50.71 Å
Envelope Rg envelope_rg	45.34 Å
Shape Rg shape_rg	46.64 Å
Total Rg total_rg	46.77 Å
Total atoms total_atoms	9204
Residues n_residues	1112
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	156.4 Å
Rg (real space) rg_real	46.96 Å
Rg uncertainty (real space) rg_real_error	1.53 Å
I(0) (real space) i0_real	2.4400e+08
I(0) uncertainty (real space) i0_real_error	4.0730e+06
Rg (reciprocal space) rg_reciprocal	46.49 Å
I(0) (reciprocal space) i0_reciprocal	243800000.0000
Solution quality estimate total_estimate	0.6870
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.2 Å
Skewness Skewness skewness	0.322
Kurtosis Kurtosis kurtosis	-1.038
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	149500000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.180; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.529; Smooth: 0.858

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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1bkoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

Domain ID domain_id	d1bkob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

Domain ID domain_id	d1bkoc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

Domain ID domain_id	d1bkod_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (4 domains)

Domain ID domain_id	1bkoA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

Domain ID domain_id	1bkoB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

Domain ID domain_id	1bkoC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

Domain ID domain_id	1bkoD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

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8. Citations (3)

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Unit-cell length a length_a	99.363 Å
Unit-cell length b length_b	52.828 Å
Unit-cell length c length_c	129.391 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.3200

Description description	THYMIDYLATE SYNTHASE A
Molecular weight formula_weight	32717.0 kDa
EC 编号 ec_number	2.1.1.45
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9239

THERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS

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

THYMIDYLATE SYNTHASE A

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (3)

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	35

fit	/app/data/saxs_computation/bk/1bko/1bko.fit
pddf	/app/data/pr_computation/bk/1bko/1bko.pr.out
profile	/app/data/saxs_computation/bk/1bko/1bko.dat