SAXSdb — 8h3x

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

Fragilysin

Bacteroides fragilis

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 9–405	Not recorded	nanobody 282 × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Potassium thiocyanate, 20 % w/v PEG 3350	Resolution 1.66 Å R-free 0.216

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 8H3X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H3Y Bacteroide Fragilis Toxin in complex with nanobody 327 Deposited 2022-10-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350, pH 6.6	Resolution 2.25 Å R-free 0.244
8H3Y Bacteroide Fragilis Toxin in complex with nanobody 327 Deposited 2022-10-09	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350, pH 6.6	Resolution 2.25 Å R-free 0.244
8H3Y Bacteroide Fragilis Toxin in complex with nanobody 327 Deposited 2022-10-09	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350, pH 6.6	Resolution 2.25 Å R-free 0.244
8WEM Bacteroides fragilis toxin 1 Deposited 2023-09-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350, 32 mg mL-1	Resolution 1.80 Å R-free 0.202
8WEM Bacteroides fragilis toxin 1 Deposited 2023-09-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–405（397 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350, 32 mg mL-1	Resolution 1.80 Å R-free 0.202
8WEO Bacteroides fragilis toxin in complex with neutralization nanobody Deposited 2023-09-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000	Resolution 1.50 Å R-free 0.197
8WEO Bacteroides fragilis toxin in complex with neutralization nanobody Deposited 2023-09-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000	Resolution 1.50 Å R-free 0.197
9XVH Crystal structure of mature Bacteroides fragilis toxin 1 Deposited 2025-11-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 21% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.	Resolution 1.94 Å R-free 0.266
9XVH Crystal structure of mature Bacteroides fragilis toxin 1 Deposited 2025-11-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 21% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.	Resolution 1.94 Å R-free 0.266
9XVH Crystal structure of mature Bacteroides fragilis toxin 1 Deposited 2025-11-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 21% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.	Resolution 1.94 Å R-free 0.266
9XVH Crystal structure of mature Bacteroides fragilis toxin 1 Deposited 2025-11-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 220–405（186 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 21% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.	Resolution 1.94 Å R-free 0.266

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

View Construct and Data Evidence

UniProt name	ENTM_BACFG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–397； UniProt 9–405

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	8h3x
Deposition date deposition_date	2022-10-09
Structure title title	Bacteroide Fragilis Toxin in complex with nanobody 282
Keywords keywords	Bacteroide Fragilis Toxin, nanobody, TOXIN; TOXIN
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	26.22 Å
Radius of gyration Rg (electron density) rg_electron	25.37 Å
Forward intensity I(0) i0	49388600.00
Molecular weight molecular_weight	53479.0 kDa
Excluded volume excluded_volume	66338 Å³
Envelope volume envelope_volume	81129 Å³
Hydration-shell volume shell_volume	27294 Å³
Envelope diameter envelope_diameter	91.7 Å
Shell Rg shell_rg	31.76 Å
Envelope Rg envelope_rg	25.80 Å
Shape Rg shape_rg	25.36 Å
Total Rg total_rg	26.06 Å
Total atoms total_atoms	3762
Residues n_residues	481
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	89.9 Å
Rg (real space) rg_real	26.27 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	4.9390e+07
I(0) uncertainty (real space) i0_real_error	7.1420e+05
Rg (reciprocal space) rg_reciprocal	26.26 Å
I(0) (reciprocal space) i0_reciprocal	49390000.0000
Solution quality estimate total_estimate	0.8760
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.5 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.312
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12540000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Fragilysin
Molecular weight formula_weight	44449.9 kDa
EC 编号 ec_number	3.4.24.74
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	4360

MKNVKLLLMLGTAALLAACSNEADSLTTSIDAPVTASIDLQSVSYTDLATQLNDVSDFGKMIILKDNGFNRQVHVSMDKRTKIQLDNENVRLFNGRDKDSTSFILGDEFAVLRFYRNGESISYIAYKEAQMMNEIAEFYAAPFKKTRAINEKEAFECIYDSRTRSAGKDIVSVKINIDKAKKILNLPECDYINDYIKTPQVPHGITESQTRAVPSEPKTVYVICLRENGSTIYPNEVSAQMQDAANSVYAVHGLKRYVNFHFVLYTTEYSCPSGDAKEGLEGFTASLKSNPKAEGYDDQIYFLIRWGTWDNKILGMSWFNSYNVNTASDFEASGMSTTQLMYPGVMAHELGHILGAEHTDNSKDLMYATFTGYLSHLSEKNMDIIAKNLGWEAADGD

来源 Source

来源生物 organism	Bacteroides fragilis
NCBI Class编号 ncbi_taxonomy_id	817
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	nanobody 282
Molecular weight formula_weight	14255.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

QVQLQESGGGLVQPGGSLRLSCAASGFTFSRYTMTWVRQAPGKGLEWVSNINSDGGRTYYADSVKGRFTISRDNTKNTLYLQMNSLKPEDTAVYYCAIPKRTYVPPSQFDDRGQGTQVTVSSHHHHHH

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	563

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8h3xA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	55.663 Å
Unit-cell length b length_b	78.212 Å
Unit-cell length c length_c	118.132 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.660 Å
Low-resolution limit resolution_low	35.170 Å
R factor r_factor	0.1843
R_work r_work	0.1832
R_free r_free	0.2164

fit	/app/data/saxs_computation/h3/8h3x/8h3x.fit
pddf	/app/data/pr_computation/h3/8h3x/8h3x.pr.out
profile	/app/data/saxs_computation/h3/8h3x/8h3x.dat

Bacteroide Fragilis Toxin in complex with nanobody 282

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

Fragilysin

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)