SAXSdb — 1tol

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

PROTEIN (FUSION PROTEIN CONSISTING OF MINOR COAT PROTEIN, GLYCINE RICH LINKER, TOLA, AND A HIS TAG)

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 19–104	Fragment：N-TERMINAL DOMAIN OF MINOR COAT PROTEIN AND C-TERMINAL DOMAIN OF TOLA	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN AT CONCENTRATION 8-12 MG/ML IN 50 MM HEPES (PH=7.5) WITH ADDITION OF DTT C=2MM, WAS CRYSTALLIZED USING VAPOR DIFFUSION FROM THE SITTING OR HANGING DROP, WITH THE SOLUTION CONTAINING 25% PEG4000, 0.08M TRIS (PH=8.5), AND 0.15 M SODIUM ACETATE AS A PRECIPITANT. BEFORE SETTING THE DROPS, PROTEIN SOLUTION WAS MIXED WITH THE PRECIPITANT IN THE RATIO 1:1. CRYSTALS WERE GROWING BEST AT TEMPERATURE 15 DEGREES CELSIUS.	Resolution 1.85 Å R-free 0.293

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A0N8P2C2_9PROT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–86； UniProt 19–104

PROTEIN (FUSION PROTEIN CONSISTING OF MINOR COAT PROTEIN, GLYCINE RICH LINKER, TOLA, AND A HIS TAG)

Escherichia coli

UniProt P19934

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 295–421	Fragment：N-TERMINAL DOMAIN OF MINOR COAT PROTEIN AND C-TERMINAL DOMAIN OF TOLA	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN AT CONCENTRATION 8-12 MG/ML IN 50 MM HEPES (PH=7.5) WITH ADDITION OF DTT C=2MM, WAS CRYSTALLIZED USING VAPOR DIFFUSION FROM THE SITTING OR HANGING DROP, WITH THE SOLUTION CONTAINING 25% PEG4000, 0.08M TRIS (PH=8.5), AND 0.15 M SODIUM ACETATE AS A PRECIPITANT. BEFORE SETTING THE DROPS, PROTEIN SOLUTION WAS MIXED WITH THE PRECIPITANT IN THE RATIO 1:1. CRYSTALS WERE GROWING BEST AT TEMPERATURE 15 DEGREES CELSIUS.	Resolution 1.85 Å R-free 0.293

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 1TOL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1S62 Solution structure of the Escherichia coli TolA C-terminal domain Deposited 2004-01-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 325–421（97 aa） Fragment：C-terminal domain (residues 325-421)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；300 K；Ionic strength (raw mmCIF value) 100mN NaCl, 50mM NaPO4；Pressure ambient NMR measurement conditions pH 6.8；300 K；Ionic strength (raw mmCIF value) 50mN NaCl, 50mM NaPO4；Pressure ambient NMR measurement conditions pH 6.8；300 K；Ionic strength (raw mmCIF value) 500mN NaCl, 50mM NaPO4；Pressure ambient NMR sample composition 1.4mM U-15N, 100mN NaCl, 50mM NaPO4, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5mM U-15N,13C, 50mN NaCl, 50mM NaPO4, Complete protease inhibitor (Boehringer), 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7mM U-15N, 500mN NaCl, 50mM NaPO4, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3QDP Structural characterization of the interaction of colicin A, colicin N, and TolB with TolAIII translocon Deposited 2011-01-19	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 302–421（120 aa） Fragment：TolA domain III, residues 302-421	Non-standard monomer：Yes (specific site not provided by mmCIF)	NO3 NITRATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.28；293 K；0.2 M NaNO3, 2.2 M ammonium sulphate, pH 5.28, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.15 Å R-free 0.225
3QDR Structural characterization of the interaction of colicin A, colicin N, and TolB with the TolAIII translocon Deposited 2011-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 302–421（120 aa） Fragment：TolA domain III, residues 302-421	Non-standard monomer：Yes (specific site not provided by mmCIF)	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M K2HPO4, 2.2 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.65 Å R-free 0.273
9DDM E. coli TolAQR conformation I Deposited 2024-08-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain F 2–421（420 aa） Chain G 2–421（420 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
9DDN E. coli TolAQR conformation II Deposited 2024-08-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain F 2–421（420 aa） Chain G 2–421（420 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9K49 Cryo-EM structure of inner membrane TolQRA complex in CYMAL-6-Neopentyl Glycol detergent micelles Deposited 2024-10-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–421（421 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Phosphate-buffered saline (PBS) buffer at pH 7.5 (20 mM PBS pH 7.5, 300 mM NaCl) with 20 mM Imidazole and 0.04 mM CYMAL-6 Neopentyl Glycol detergent cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9KCH Cryo-EM structure of inner membrane TolQRA complex in CYMAL-6-Neopentyl Glycol detergent micelles Deposited 2024-11-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–421（421 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Phosphate-buffered saline (PBS) buffer at pH 7.5 (20 mM PBS pH 7.5, 300 mM NaCl) with 20 mM Imidazole and 0.04 mM CYMAL-6 Neopentyl Glycol detergent cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.19 Å
9KPZ Structure of TolQRA complex at pH 5.4 from E.coli Deposited 2024-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 2–421（420 aa） Chain I 2–421（420 aa） Chain J 2–421（420 aa） Chain K 2–421（420 aa） Chain L 2–421（420 aa）	Not recorded	3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 5.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9KQ0 Structure of TolQRA complex at pH 8.0 from E.coli Deposited 2024-11-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 2–421（420 aa） Chain I 2–421（420 aa） Chain J 2–421（420 aa） Chain K 2–421（420 aa） Chain L 2–421（420 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9QUQ cryo-EM structure of TolQR conformation2 in SMA nanodiscs Deposited 2025-04-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–421（421 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
9QVD cryo-EM structure of TolQRA in nanodiscs Deposited 2025-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain H 1–421（421 aa） Chain I 1–421（421 aa） Chain J 1–421（421 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOLA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 87–213； UniProt 295–421

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	1tol
Deposition date deposition_date	1999-05-17
Structure title title	FUSION OF N-TERMINAL DOMAIN OF THE MINOR COAT PROTEIN FROM GENE III IN PHAGE M13, AND C-TERMINAL DOMAIN OF E. COLI PROTEIN-TOLA
Keywords keywords	BACTERIOPHAGE M13, PHAGE INFECTION, TOL PATHWAY, FUSION PROTEIN, Viral protein; VIRAL PROTEIN
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	16.26 Å
Radius of gyration Rg (electron density) rg_electron	15.43 Å
Forward intensity I(0) i0	5307990.00
Molecular weight molecular_weight	16677.0 kDa
Excluded volume excluded_volume	20897 Å³
Envelope volume envelope_volume	23535 Å³
Hydration-shell volume shell_volume	13232 Å³
Envelope diameter envelope_diameter	54.2 Å
Shell Rg shell_rg	20.92 Å
Envelope Rg envelope_rg	15.78 Å
Shape Rg shape_rg	15.38 Å
Total Rg total_rg	16.58 Å
Total atoms total_atoms	1172
Residues n_residues	157
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	56.0 Å
Rg (real space) rg_real	16.21 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	5.3080e+06
I(0) uncertainty (real space) i0_real_error	5.5580e+04
Rg (reciprocal space) rg_reciprocal	16.21 Å
I(0) (reciprocal space) i0_reciprocal	5308000.0000
Solution quality estimate total_estimate	0.8651
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.295
Kurtosis Kurtosis kurtosis	-0.202
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1130000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.984

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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) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1tola1
Class class	b — All beta proteins
Fold Fold fold	b.37 — N-terminal domains of the minor coat protein g3p
Superfamily Superfamily superfamily	b.37.1 — N-terminal domains of the minor coat protein g3p
Family Family family	b.37.1.1 — N-terminal domains of the minor coat protein g3p

Domain ID domain_id	d1tola2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.212 — TolA/TonB C-terminal domain
Superfamily Superfamily superfamily	d.212.1 — TolA/TonB C-terminal domain
Family Family family	d.212.1.1 — TolA

Domain ID domain_id	d1tola3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1tolA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	27 — Phage FD Coat Protein, Membrane penetration domain
Homologous superfamily homologous superfamily	10 — Phage FD Coat Protein,Membrane penetration domain

Domain ID domain_id	1tolA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1150 — Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	88.880 Å
Unit-cell length b length_b	88.880 Å
Unit-cell length c length_c	63.556 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2275
R_work r_work	—
R_free r_free	0.2930

Description description	PROTEIN (FUSION PROTEIN CONSISTING OF MINOR COAT PROTEIN, GLYCINE RICH LINKER, TOLA, AND A HIS TAG)
Molecular weight formula_weight	22851.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1331

FUSION OF N-TERMINAL DOMAIN OF THE MINOR COAT PROTEIN FROM GENE III IN PHAGE M13, AND C-TERMINAL DOMAIN OF E. COLI PROTEIN-TOLA

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

PROTEIN (FUSION PROTEIN CONSISTING OF MINOR COAT PROTEIN, GLYCINE RICH LINKER, TOLA, AND A HIS TAG)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (FUSION PROTEIN CONSISTING OF MINOR COAT PROTEIN, GLYCINE RICH LINKER, TOLA, AND A HIS TAG)

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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
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	159

fit	/app/data/saxs_computation/to/1tol/1tol.fit
pddf	/app/data/pr_computation/to/1tol/1tol.pr.out
profile	/app/data/saxs_computation/to/1tol/1tol.dat