SAXSdb — 1c5k

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

PROTEIN (TOLB PROTEIN)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–430	Fragment：ENTIRE PROTEIN	YB YTTERBIUM (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.271

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 1C5K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CRZ CRYSTAL STRUCTURE OF THE E. COLI TOLB PROTEIN Deposited 1999-08-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–430（403 aa）	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；293 K；PEG 8000, SODIUM CHLORIDE, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.95 Å R-free 0.238
2HQS Crystal structure of TolB/Pal complex Deposited 2006-07-19	Different construct 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 23–430（408 aa）	Not recorded	ACT ACETATE ION × 2 SO4 SULFATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；MME PEG 2000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.213
2HQS Crystal structure of TolB/Pal complex Deposited 2006-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–430（408 aa）	Not recorded	ACT ACETATE ION × 2 SO4 SULFATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；MME PEG 2000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.213
2HQS Crystal structure of TolB/Pal complex Deposited 2006-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–430（408 aa）	Not recorded	ACT ACETATE ION × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；MME PEG 2000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.213
2HQS Crystal structure of TolB/Pal complex Deposited 2006-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 23–430（408 aa）	Not recorded	ACT ACETATE ION × 2 SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；MME PEG 2000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.213
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23	Different construct 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 1–430（430 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5	Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–430（430 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5	Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–430（430 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5	Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–430（430 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5	Resolution 2.00 Å R-free 0.222
2W8B Crystal structure of processed TolB in complex with Pal Deposited 2009-01-15	Different construct 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 22–430（409 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M SODIUM ACETATE PH 4.6, 17% PEG4000, 0.2M AMMONIUM SULPHATE, 20MG/ML	Resolution 1.86 Å R-free 0.247
2W8B Crystal structure of processed TolB in complex with Pal Deposited 2009-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 22–430（409 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M SODIUM ACETATE PH 4.6, 17% PEG4000, 0.2M AMMONIUM SULPHATE, 20MG/ML	Resolution 1.86 Å R-free 0.247
2W8B Crystal structure of processed TolB in complex with Pal Deposited 2009-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 22–430（409 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M SODIUM ACETATE PH 4.6, 17% PEG4000, 0.2M AMMONIUM SULPHATE, 20MG/ML	Resolution 1.86 Å R-free 0.247
2W8B Crystal structure of processed TolB in complex with Pal Deposited 2009-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 22–430（409 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M SODIUM ACETATE PH 4.6, 17% PEG4000, 0.2M AMMONIUM SULPHATE, 20MG/ML	Resolution 1.86 Å R-free 0.247
3IAX The crystal structure of the TolB box of Colicin A in complex with TolB reveals important differences in the recruitment of the common TolB translocation portal used by group A colicins Deposited 2009-07-15	Different construct 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 1–430（430 aa）	Not recorded	NA SODIUM ION × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 10000, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.257

5 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOLB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–431； UniProt 1–430

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	1c5k
Deposition date deposition_date	1999-12-05
Structure title title	THE STRUCTURE OF TOLB, AN ESSENTIAL COMPONENT OF THE TOL-DEPENDENT TRANSLOCATION SYSTEM AND ITS INTERACTIONS WITH THE TRANSLOCATION DOMAIN OF COLICIN E9
Keywords keywords	BETA PROPELLOR, PROTEIN-PROTEIN INTERACTIONS, COLICIN IMPORT, TRANSPORT PROTEIN; TRANSPORT 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	23.47 Å
Radius of gyration Rg (electron density) rg_electron	22.54 Å
Forward intensity I(0) i0	32453300.00
Molecular weight molecular_weight	42487.0 kDa
Excluded volume excluded_volume	52606 Å³
Envelope volume envelope_volume	62536 Å³
Hydration-shell volume shell_volume	23615 Å³
Envelope diameter envelope_diameter	79.2 Å
Shell Rg shell_rg	29.04 Å
Envelope Rg envelope_rg	22.79 Å
Shape Rg shape_rg	22.55 Å
Total Rg total_rg	23.30 Å
Total atoms total_atoms	2991
Residues n_residues	397
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	78.0 Å
Rg (real space) rg_real	23.48 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	3.2450e+07
I(0) uncertainty (real space) i0_real_error	4.7950e+05
Rg (reciprocal space) rg_reciprocal	23.48 Å
I(0) (reciprocal space) i0_reciprocal	32450000.0000
Solution quality estimate total_estimate	0.8854
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.382
Kurtosis Kurtosis kurtosis	-0.314
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9539000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (TOLB PROTEIN)
Molecular weight formula_weight	47196.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3221

MMKQALRVAFGFLILWASVLHAEVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPSLAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYLLEHHHHHH

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	YTTERBIUM (III) ION
Molecular weight formula_weight	173.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	230

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c5ka1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.4 — TolB, C-terminal domain
Family Family family	b.68.4.1 — TolB, C-terminal domain

Domain ID domain_id	d1c5ka2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.2 — TolB, N-terminal domain
Family Family family	c.51.2.1 — TolB, N-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1c5kA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10070 — TolB, N-terminal domain

Domain ID domain_id	1c5kA02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	63.580 Å
Unit-cell length b length_b	40.190 Å
Unit-cell length c length_c	77.660 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2710

fit	/app/data/saxs_computation/c5/1c5k/1c5k.fit
pddf	/app/data/pr_computation/c5/1c5k/1c5k.pr.out
profile	/app/data/saxs_computation/c5/1c5k/1c5k.dat

THE STRUCTURE OF TOLB, AN ESSENTIAL COMPONENT OF THE TOL-DEPENDENT TRANSLOCATION SYSTEM AND ITS INTERACTIONS WITH THE TRANSLOCATION DOMAIN OF COLICIN E9

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

PROTEIN (TOLB PROTEIN)

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