SAXSdb — 6suf

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

TcdA1

Photorhabdus luminescens

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 Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–2516 Chain B； UniProt 1–2516 Chain C； UniProt 1–2516 Chain D； UniProt 1–2516 Chain E； UniProt 1–2516	Not recorded	TcdB2,TccC3 × 1 （Q8GF99,Q8GF97）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 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 6SUF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4O9Y Crystal Structure of TcdA1 Deposited 2014-01-03	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES pH 7.0, 0.1 % Jeffamine ED-2001 and 1.1 M sodium malonate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.295
4O9Y Crystal Structure of TcdA1 Deposited 2014-01-03	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 1–2516（2516 aa） Chain G 1–2516（2516 aa） Chain H 1–2516（2516 aa） Chain I 1–2516（2516 aa） Chain J 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M HEPES pH 7.0, 0.1 % Jeffamine ED-2001 and 1.1 M sodium malonate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.295
5LKH Cryo-EM structure of the Tc toxin TcdA1 in its pore state (obtained by flexible fitting) Deposited 2016-07-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 11 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
5LKI Cryo-EM structure of the Tc toxin TcdA1 in its pore state Deposited 2016-07-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 11 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
6H6E PTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1, TcdB2, TccC3) Deposited 2018-07-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 3 sec before plunging	Resolution 3.95 Å
6H6F PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A Deposited 2018-07-27	Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
6L7E Toxin Complex TcdA1-TcdB1-TccC2 Deposited 2019-11-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6L7I Signal substraction of TcdB1-TccC2 and part of TcdA1 Deposited 2019-11-01	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 2327–2516（190 aa） Chain B 2327–2516（190 aa） Chain C 2327–2516（190 aa） Chain D 2327–2516（190 aa） Chain E 2327–2516（190 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
6RW6 Cryo-EM structure of Photorhabdus luminescens TcdA1 Deposited 2019-06-04	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.75 Å
6SUE Structure of Photorhabdus luminescens Tc holotoxin pore, Mutation TccC3-D651A Deposited 2019-09-13	Parsed fields agree	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8CPZ Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K1179W mutant Deposited 2023-03-03	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Mutation：K1179W Mutation：K1179W Mutation：K1179W Mutation：K1179W Mutation：K1179W	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 11.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8CQ0 Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K567W K2008W mutant Deposited 2023-03-03	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Mutation：K567W K2008W Mutation：K567W K2008W Mutation：K567W K2008W Mutation：K567W K2008W Mutation：K567W K2008W	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 11.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8CQ2 Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S, C20S, C870S, T1279C mutant Deposited 2023-03-03	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–2516（2516 aa） Chain B 1–2516（2516 aa） Chain C 1–2516（2516 aa） Chain D 1–2516（2516 aa） Chain E 1–2516（2516 aa）	Mutation：C16S C20S C870S T1279C Mutation：C16S C20S C870S T1279C Mutation：C16S C20S C870S T1279C Mutation：C16S C20S C870S T1279C Mutation：C16S C20S C870S T1279C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 11.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9RN43_PHOLU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–2516； UniProt 1–2516 Author chain B； PDBConstruct 1–2516； UniProt 1–2516 Author chain C； PDBConstruct 1–2516； UniProt 1–2516 Author chain D； PDBConstruct 1–2516； UniProt 1–2516 Author chain E； PDBConstruct 1–2516； UniProt 1–2516

TcdB2,TccC3

Photorhabdus luminescens

UniProt Q8GF97

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 Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain F； UniProt 1–960	Not recorded	TcdA1 × 5 （Q9RN43）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 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 6SUF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4O9X Crystal Structure of TcdB2-TccC3 Deposited 2014-01-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–678（678 aa） Fragment：UNP Q8GF97 RESIDUES 1-678	Not recorded	HG MERCURY (II) ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Trisodium citrate pH 5.5, 0.1 M MgCl2, 0.1 M NaCl and 12 % PEG 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.17 Å R-free 0.215
6H6E PTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1, TcdB2, TccC3) Deposited 2018-07-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–960（960 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 3 sec before plunging	Resolution 3.95 Å
6H6F PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A Deposited 2018-07-27	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–860（860 aa） Chain F 861–960（100 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
6H6G Crystal Structure of TcdB2-TccC3 without hypervariable C-terminal region Deposited 2018-07-27	Different construct 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 1–678（678 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M tri-sodium citrate pH 5.5, 10 % PEG 8000, 10 % ethylenglycol	Resolution 3.00 Å R-free 0.253
6SUE Structure of Photorhabdus luminescens Tc holotoxin pore, Mutation TccC3-D651A Deposited 2019-09-13	Parsed fields agree	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–960（960 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6SUP Crystal Structure of TcdB2-TccC3-Cdc42 Deposited 2019-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–678（644 aa）	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293.15 K；0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000 Seeding: 0.1 M magnesium chloride, 0.1 M tri-sodium acetate pH 4.6, 12 % PEG 6000	Resolution 2.00 Å R-free 0.320
6SUQ Crystal Structure of TcdB2-TccC3-TEV Deposited 2019-09-16	Different construct 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 1–680（680 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000	Resolution 3.70 Å R-free 0.302
7Z7H Structure of P. luminescens TccC3-F-actin complex Deposited 2022-03-15	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 779–960（182 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 NCA NICOTINAMIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7ZBQ Structure of the ADP-ribosyltransferase TccC3HVR from Photorhabdus Luminescens Deposited 2022-03-24	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 776–960（185 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.8；280 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition 500 uM non-exchangeable-D, U-13C, U-15N TcART, 20 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 500 uM [U-13C; U-15N] TcART, 20 mM d11-Tris, 150 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 500 uM [U-13C; U-15N] TcART, 20 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8GF97_PHOLU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1480–2439； UniProt 1–960

TcdB2,TccC3

Photorhabdus luminescens

UniProt Q8GF99

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 Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain F； UniProt 1–1474	Not recorded	TcdA1 × 5 （Q9RN43）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 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 6SUF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4O9X Crystal Structure of TcdB2-TccC3 Deposited 2014-01-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1474（1474 aa） Fragment：UNP Q8GF97 RESIDUES 1-678	Not recorded	HG MERCURY (II) ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Trisodium citrate pH 5.5, 0.1 M MgCl2, 0.1 M NaCl and 12 % PEG 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.17 Å R-free 0.215
6H6E PTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1, TcdB2, TccC3) Deposited 2018-07-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–1474（1474 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot 3 sec before plunging	Resolution 3.95 Å
6H6F PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A Deposited 2018-07-27	Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–1474（1474 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
6H6G Crystal Structure of TcdB2-TccC3 without hypervariable C-terminal region Deposited 2018-07-27	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 1–1474（1474 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M tri-sodium citrate pH 5.5, 10 % PEG 8000, 10 % ethylenglycol	Resolution 3.00 Å R-free 0.253
6SUE Structure of Photorhabdus luminescens Tc holotoxin pore, Mutation TccC3-D651A Deposited 2019-09-13	Parsed fields agree	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–1474（1474 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6SUP Crystal Structure of TcdB2-TccC3-Cdc42 Deposited 2019-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–1471（1440 aa）	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293.15 K；0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000 Seeding: 0.1 M magnesium chloride, 0.1 M tri-sodium acetate pH 4.6, 12 % PEG 6000	Resolution 2.00 Å R-free 0.320
6SUQ Crystal Structure of TcdB2-TccC3-TEV Deposited 2019-09-16	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 1–1474（1474 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000	Resolution 3.70 Å R-free 0.302

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8GF99_PHOLU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1–1474； UniProt 1–1474

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	6suf
Deposition date deposition_date	2019-09-13
Structure title title	Structure of Photorhabdus luminescens Tc holotoxin pore
Keywords keywords	Complex, Holotoxin, Photorhabdus, Insecticidal, Translocation, TOXIN; TOXIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	82.98 Å
Radius of gyration Rg (electron density) rg_electron	82.49 Å
Forward intensity I(0) i0	32479400000.00
Molecular weight molecular_weight	1531900.0 kDa
Excluded volume excluded_volume	1912900 Å³
Envelope volume envelope_volume	3033300 Å³
Hydration-shell volume shell_volume	297510 Å³
Envelope diameter envelope_diameter	355.2 Å
Shell Rg shell_rg	89.77 Å
Envelope Rg envelope_rg	81.17 Å
Shape Rg shape_rg	82.49 Å
Total Rg total_rg	82.54 Å
Total atoms total_atoms	108112
Residues n_residues	13607
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	209.4 Å
Rg (real space) rg_real	78.12 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.0930e+10
I(0) uncertainty (real space) i0_real_error	5.4550e+08
Rg (reciprocal space) rg_reciprocal	82.92 Å
I(0) (reciprocal space) i0_reciprocal	32480000000.0000
Solution quality estimate total_estimate	0.9120
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	99.2 Å
Skewness Skewness skewness	0.110
Kurtosis Kurtosis kurtosis	-0.540
Angular range angular_range	— – 0.0950 Å⁻¹
Current regularization parameter α current_alpha	0.2594
Highest regularization parameter α highest_alpha	6144000000.0000
Real-space data points n_real_points	20
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.002; Oscil: 0.992; Stabil: 0.987; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	TcdA1
Molecular weight formula_weight	283230.4 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	108112

MNESVKEIPDVLKSQCGFNCLTDISHSSFNEFRQQVSEHLSWSETHDLYHDAQQAQKDNRLYEARILKRANPQLQNAVHLAILAPNAELIGYNNQFSGRASQYVAPGTVSSMFSPAAYLTELYREARNLHASDSVYYLDTRRPDLKSMALSQQNMDIELSTLSLSNELLLESIKTESKLENYTKVMEMLSTFRPSGATPYHDAYENVREVIQLQDPGLEQLNASPAIAGLMHQASLLGINASISPELFNILTEEITEGNAEELYKKNFGNIEPASLAMPEYLKRYYNLSDEELSQFIGKASNFGQQEYSNNQLITPVVNSSDGTVKVYRITREYTTNAYQMDVELFPFGGENYRLDYKFKNFYNASYLSIKLNDKRELVRTEGAPQVNIEYSANITLNTADISQPFEIGLTRVLPSGSWAYAAAKFTVEEYNQYSFLLKLNKAIRLSRATELSPTILEGIVRSVNLQLDINTDVLGKVFLTKYYMQRYAIHAETALILCNAPISQRSYDNQPSQFDRLFNTPLLNGQYFSTGDEEIDLNSGSTGDWRKTILKRAFNIDDVSLFRLLKITDHDNKDGKIKNNLKNLSNLYIGKLLADIHQLTIDELDLLLIAVGEGKTNLSAISDKQLATLIRKLNTITSWLHTQKWSVFQLFIMTSTSYNKTLTPEIKNLLDTVYHGLQGFDKDKADLLHVMAPYIAATLQLSSENVAHSVLLWADKLQPGDGAMTAEKFWDWLNTKYTPGSSEAVETQEHIVQYCQALAQLEMVYHSTGINENAFRLFVTKPEMFGAATGAAPAHDALSLIMLTRFADWVNALGEKASSVLAAFEANSLTAEQLADAMNLDANLLLQASIQAQNHQHLPPVTPENAFSCWTSINTILQWVNVAQQLNVAPQGVSALVGLDYIESMKETPTYAQWENAAGVLTAGLNSQQANTLHAFLDESRSAALSTYYIRQVAKAAAAIKSRDDLYQYLLIDNQVSAAIKTTRIAEAIASIQLYVNRALENVEENANSGVISRQFFIDWDKYNKRYSTWAGVSQLVYYPENYIDPTMRIGQTKMMDALLQSVSQSQLNADTVEDAFMSYLTSFEQVANLKVISAYHDNINNDQGLTYFIGLSETDAGEYYWRSVDHSKFNDGKFAANAWSEWHKIDCPINPYKSTIRPVIYKSRLYLLWLEQKEITKQTGNSKDGYQTETDYRYELKLAHIRYDGTWNTPITFDVNKKISELKLEKNRAPGLYCAGYQGEDTLLVMFYNQQDTLDSYKNASMQGLYIFADMASKDMTPEQSNVYRDNSYQQFDTNNVRRVNNRYAEDYEIPSSVSSRKDYGWGDYYLSMVYNGDIPTINYKAASSDLKIYISPKLRIIHNGYEGQKRNQCNLMNKYGKLGDKFIVYTSLGVNPNNSSNKLMFYPVYQYSGNTSGLNQGRLLFHRDTTYPSKVEAWIPGAKRSLTNQNAAIGDDYATDSLNKPDDLKQYIFMTDSKGTATDVSGPVEINTAISPAKVQIIVKAGGKEQTFTADKDVSIQPSPSFDEMNYQFNALEIDGSGLNFINNSASIDVTFTAFAEDGRKLGYESFSIPVTLKVSTDNALTLHHNENGAQYMQWQSYRTRLNTLFARQLVARATTGIDTILSMETQNIQEPQLGKGFYATFVIPPYNLSTHGDERWFKLYIKHVVDNNSHIIYSGQLTDTNINITLFIPLDDVPLNQDYHAKVYMTFKKSPSDGTWWGPHFVRDDKGIVTINPKSILTHFESVNVLNNISSEPMDFSGANSLYFWELFYYTPMLVAQRLLHEQNFDEANRWLKYVWSPSGYIVHGQIQNYQWNVRPLLEDTSWNSDPLDSVDPDAVAQHDPMHYKVSTFMRTLDLLIARGDHAYRQLERDTLNEAKMWYMQALHLLGDKPYLPLSTTWSDPRLDRAADITTQNAHDSAIVALRQNIPTPAPLSLRSANTLTDLFLPQINEVMMNYWQTLAQRVYNLRHNLSIDGQPLYLPIYATPADPKALLSAAVATSQGGGKLPESFMSLWRFPHMLENARGMVSQLTQFGSTLQNIIERQDAEALNALLQNQAAELILTNLSIQDKTIEELDAEKTVLEKSKAGAQSRFDSYGKLYDENINAGENQAMTLRASAAGLTTAVQASRLAGAAADLVPNIFGFAGGGSRWGAIAEATGYVMEFSANVMNTEADKISQSETYRRRRQEWEIQRNNAEAELKQIDAQLKSLAVRREAAVLQKTSLKTQQEQTQSQLAFLQRKFSNQALYNWLRGRLAAIYFQFYDLAVARCLMAEQAYRWELNDDSARFIKPGAWQGTYAGLLAGETLMLSLAQMEDAHLKRDKRALEVERTVSLAEVYAGLPKDNGPFSLAQEIDKLVSQGSGSAGSGNNNLAFGAGTDTKTSLQASVSFADLKIREDYPASLGKIRRIKQISVTLPALLGPYQDVQAILSYGDKAGLANGCEALAVSHGMNDSGQFQLDFNDGKFLPFEGIAIDQGTLTLSFPNASMPEKGKQATMLKTLNDIILHIRYTIK

来源 Source

来源生物 organism	Photorhabdus luminescens
NCBI Class编号 ncbi_taxonomy_id	29488
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TcdB2,TccC3
Molecular weight formula_weight	274188.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MQNSQDFSITELSLPKGGGAITGMGEALTPTGPDGMAALSLPLPISAGRGYAPAFTLNYNSGAGNSPFGLGWDCNVMTIRRRTHFGVPHYDETDTFLGPEGEVLVVADQPRDESTLQGINLGATFTVTGYRSRLESHFSRLEYWQPKTTGKTDFWLIYSPDGQVHLLGKSPQARISNPSQTTQTAQWLLEASVSSRGEQIYYQYRAEDDTGCEADEITHHLQATAQRYLHIVYYGNRTASETLPGLDGSAPSQADWLFYLVFDYGERSNNLKTPPAFSTTGSWLCRQDRFSRYEYGFEIRTRRLCRQVLMYHHLQALDSKITEHNGPTLVSRLILNYDESAIASTLVFVRRVGHEQDGNVVTLPPLELAYQDFSPRHHAHWQPMDVLANFNAIQRWQLVDLKGEGLPGLLYQDKGAWWYRSAQRLGEIGSDAVTWEKMQPLSVIPSLQSNASLVDINGDGQLDWVITGPGLRGYHSQRPDGSWTRFTPLNALPVEYTHPRAQLADLMGAGLSDLVLIGPKSVRLYANTRDGFAKGKDVVQSGEITLPVPGADPRKLVAFSDVLGSGQAHLVEVSATKVTCWPNLGRGRFGQPITLPGFSQPATEFNPAQVYLADLDGSGPTDLIYVHTNRLDIFLNKSGNGFAEPVTLRFPEGLRFDHTCQLQMADVQGLGVASLILSVPHMSPHHWRCDLTNMKPWLLNEMNNNMGVHHTLRYRSSSQFWLDEKAAALTTGQTPVCYLPFPIHTLWQTETEDEISGNKLVTTLRYARGAWDGREREFRGFGYVEQTDSHQLAQGNAPERTPPALTKNWYATGLPVIDNALSTEYWRDDQAFAGFSPRFTTWQDNKDVPLTPEDDNSRYWFNRALKGQLLRSELYGLDDSTNKHVPYTVTEFRSQVRRLQHTDSRYPVLWSSVVESRNYHYERIASDPQCSQNITLSSDRFGQPLKQLSVQYPRRQQPAINLYPDTLPDKLLANSYDDQQRQLRLTYQQSSWHHLTNNTVRVLGLPDSTRSDIFTYGAENVPAGGLNLELLSDKNSLIADDKPREYLGQQKTAYTDGQNTTPLQTPTRQALIAFTETTVFNQSTLSAFNGSIPSDKLSTTLEQAGYQQTNYLFPRTGEDKVWVAHHGYTDYGTAAQFWRPQKQSNTQLTGKITLIWDANYCVVVQTRDAAGLTTSAKYDWRFLTPVQLTDINDNQHLITLDALGRPITLRFWGTENGKMTGYSSPEKASFSPPSDVNAAIELKKPLPVAQCQVYAPESWMPVLSQKTFNRLAEQDWQKLYNARIITEDGRICTLAYRRWVQSQKAIPQLISLLNNGPRLPPHSLTLTTDRYDHDPEQQIRQQVVFSDGFGRLLQAAARHEAGMARQRNEDGSLIINVQHTENRWAVTGRTEYDNKGQPIRTYQPYFLNDWRYVSNDSARQEKEAYADTHVYDPIGREIKVITAKGWFRRTLFTPWFTVNEDENDTAAEVKKVKMPGSRPMKNIDPKLYQKTPTVSVYDNRGLIIRNIDFHRTTANGDPDTRITRHQYDIHGHLNQSIDPRLYEAKQTNNTIKPNFLWQYDLTGNPLCTESIDAGRTVTLNDIEGRPLLTVTATGVIQTRQYETSSLPGRLLSVAEQTPEEKTSRITERLIWAGNTEAEKDHNLAGQCVRHYDTAGVTRLESLSLTGTVLSQSSQLLIDTQEANWTGDNETVWQNMLADDIYTTLSTFDATGALLTQTDAKGNIQRLAYDVAGQLNGSWLTLKGQTEQVIIKSLTYSAAGQKLREEHGNDVITEYSYEPETQRLIGIKTRRPSDTKVLQDLRYEYDPVGNVISIRNDAEATRFWHNQKVMPENTYTYDSLYQLISATGREMANIGQQSHQFPSPALPSDNNTYTNYTRTYTYDRGGNLTKIQHSSPATQNNYTTNITVSNRSNRAVLSTLTEDPAQVDALFDAGGHQNTLISGQNLNWNTRGELQQVTLVKRDKGANDDREWYRYSGDGRRMLKINEQQASNNAQTQRVTYLPNLELRLTQNSTATTEDLQVITVGEAGRAQVRVLHWESGKPEDIDNNQLRYSYDNLIGSSQLELDSEGQIISEEEYYPYGGTALWAARNQTEASYKTIRYSGKERDATGLYYYGYRYYQPWIGRWLSSDPAGTIDGLNLYRMVRNNPVTLLDPDGLMPTIAERIAALKKNKVTDSAPSPANATNVAINIRPPVAPKPSLPKASTSSQPTTHPIGAANIKPTTSGSSIVAPLSPVGNKSTSEISLPESAQSSSSSTTSTNLQKKSFTLYRADNRSFEEMQSKFPEGFKAWTPLDTKMARQFASIFIGQKDTSNLPKETVKNISTWGAKPKLKDLSNYIKYTKDKSTVWVSTAINTEAGGQSSGAPLHKIDMDLYEFAIDGQKLNPLPEGRTKNMVPSLLLDTPQIETSSIIALNHGPVNDAEISFLTTIPLKNVKPHKR

来源 Source

来源生物 organism	Photorhabdus luminescens
NCBI Class编号 ncbi_taxonomy_id	29488
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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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	1

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

Resolution resolution	3.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	64806

fit	/app/data/saxs_computation/su/6suf/6suf.fit
pddf	/app/data/pr_computation/su/6suf/6suf.pr.out
profile	/app/data/saxs_computation/su/6suf/6suf.dat

Structure of Photorhabdus luminescens Tc holotoxin pore

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

TcdA1

State in the Current Structure

Other States of the Same Protein in the Database

TcdB2,TccC3

State in the Current Structure

Other States of the Same Protein in the Database

TcdB2,TccC3

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)