SAXSdb — 9ddm

▼

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

Tol-Pal system protein TolQ

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	Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 1–230 Chain B； UniProt 1–230 Chain C； UniProt 1–230 Chain D； UniProt 1–230 Chain E； UniProt 1–230	Not recorded	Tol-Pal system protein TolA × 2 （P19934） Tol-Pal system protein TolR × 2 （P0ABV8）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.94 Å

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 9DDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9DDN E. coli TolAQR conformation II Deposited 2024-08-28	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–230（230 aa） Chain B 1–230（230 aa） Chain C 1–230（230 aa） Chain D 1–230（230 aa） Chain E 1–230（230 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOLQ_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–230； UniProt 1–230 Author chain B； PDBConstruct 1–230； UniProt 1–230 Author chain C； PDBConstruct 1–230； UniProt 1–230 Author chain D； PDBConstruct 1–230； UniProt 1–230 Author chain E； PDBConstruct 1–230； UniProt 1–230

Tol-Pal system protein TolA

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	Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain F； UniProt 2–421 Chain G； UniProt 2–421	Not recorded	Tol-Pal system protein TolQ × 5 （P0ABV0） Tol-Pal system protein TolR × 2 （P0ABV8）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.94 Å

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 9DDM	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 mutation/modification 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
1TOL 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 Deposited 1999-05-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 295–421（127 aa） Fragment：N-TERMINAL DOMAIN OF MINOR COAT PROTEIN AND C-TERMINAL DOMAIN OF TOLA	Not recorded	No recorded non-water small molecule	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
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 method 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 method 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
9DDN E. coli TolAQR conformation II Deposited 2024-08-28	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 mutation/modification Different oligomeric state 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 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	2
Chains and sequence ranges	Author chain F； PDBConstruct 14–433； UniProt 2–421 Author chain G； PDBConstruct 14–433； UniProt 2–421

Tol-Pal system protein TolR

Escherichia coli

UniProt P0ABV8

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain Y； UniProt 1–142 Chain Z； UniProt 1–142	Not recorded	Tol-Pal system protein TolQ × 5 （P0ABV0） Tol-Pal system protein TolA × 2 （P19934）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.94 Å

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 9DDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9DDN E. coli TolAQR conformation II Deposited 2024-08-28	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain Y 1–142（142 aa） Chain Z 1–142（142 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOLR_ECO57
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Y； PDBConstruct 1–142； UniProt 1–142 Author chain Z； PDBConstruct 1–142； UniProt 1–142

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ddm
Deposition date deposition_date	2024-08-28
Structure title title	E. coli TolAQR conformation I
Keywords keywords	Tol-Pal system, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.84 Å
Radius of gyration Rg (electron density) rg_electron	34.12 Å
Forward intensity I(0) i0	255639000.00
Molecular weight molecular_weight	135850.0 kDa
Excluded volume excluded_volume	173330 Å³
Envelope volume envelope_volume	230660 Å³
Hydration-shell volume shell_volume	55033 Å³
Envelope diameter envelope_diameter	110.8 Å
Shell Rg shell_rg	42.03 Å
Envelope Rg envelope_rg	33.59 Å
Shape Rg shape_rg	34.11 Å
Total Rg total_rg	34.77 Å
Total atoms total_atoms	9582
Residues n_residues	1221
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

▼

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

Maximum dimension Dmax dmax	105.3 Å
Rg (real space) rg_real	34.71 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.5560e+08
I(0) uncertainty (real space) i0_real_error	3.2140e+06
Rg (reciprocal space) rg_reciprocal	34.80 Å
I(0) (reciprocal space) i0_reciprocal	255700000.0000
Solution quality estimate total_estimate	0.8779
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.1 Å
Skewness Skewness skewness	0.224
Kurtosis Kurtosis kurtosis	-0.449
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38030000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.575

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Tol-Pal system protein TolQ
Molecular weight formula_weight	25623.7 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	9582

MTDMNILDLFLKASLLVKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELSRLYQESQGKRDNLTGSEQIFYSGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELENLETHIPFLGTVGSISPYIGLFGTVWGIMHAFIALGAVKQATLQMVAPGIAEALIATAIGLFAAIPAVMAYNRLNQRVNKLELNYDNFMEEFTAILHRQAFTVSESNKG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tol-Pal system protein TolA
Molecular weight formula_weight	44563.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G

MGSWSHPQFEKGSSKATEQNDKLKRAIIISAVLHVILFAALIWSSFDENIEASAGGGGGSSIDAVMVDSGAVVEQYKRMQSQESSAKRSDEQRKMKEQQAAEELREKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAELKQKQAEEAAAKAAADAKAKAEADAKAAEEAAKKAAADAKKKAEAEAAKAAAEAQKKAEAAAAALKKKAEAAEAAAAEARKKAATEAAEKAKAEAEKKAAAEKAAADKKAAAEKAAADKKAAEKAAAEKAAADKKAAAEKAAADKKAAAAKAAAEKAAAAKAAAEADDIFGELSSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADINNYAGQIKSAIESKFYDASSYAGKTCTLRIKLAPDGMLLDIKPEGGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Tol-Pal system protein TolR
Molecular weight formula_weight	15398.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,Z

MARARGRGRRDLKSEINIVPLLDVLLVLLLIFMATAPIITQSVEVDLPDATESQAVSSNDNPPVIVEVSGIGQYTVVVEKDRLERLPPEQVVAEVSSRFKANPKTVFLIGGAKDVPYDEIIKALNLLHSAGVKSVGLMTQPI

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.94 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	59369

fit	/app/data/saxs_computation/dd/9ddm/9ddm.fit
pddf	/app/data/pr_computation/dd/9ddm/9ddm.pr.out
profile	/app/data/saxs_computation/dd/9ddm/9ddm.dat

E. coli TolAQR conformation I

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

Tol-Pal system protein TolQ

State in the Current Structure

Other States of the Same Protein in the Database

Tol-Pal system protein TolA

State in the Current Structure

Other States of the Same Protein in the Database

Tol-Pal system protein TolR

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)