SAXSdb — 1fvu

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

BOTROCETIN ALPHA CHAIN

OrganismNot specified

UniProt P22029

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–133 Chain C； UniProt 1–133	Not recorded	BOTROCETIN BETA CHAIN × 2 （P22030） MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；PEG 4000, PEG 400 and MgCl2, pH 8.5. VAPOR DIFFUSION, HANGING DROP at 295 K	Resolution 1.80 Å R-free 0.218

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 1FVU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IJK The von Willebrand Factor mutant (I546V) A1 domain-botrocetin Complex Deposited 2001-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–133（133 aa） Fragment：a-subunit	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.279
1U0N The ternary von Willebrand Factor A1-glycoprotein Ibalpha-botrocetin complex Deposited 2004-07-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–133（133 aa） Fragment：Alpha chain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；Sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.95 Å R-free 0.276
1U0O The mouse von Willebrand Factor A1-botrocetin complex Deposited 2004-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–133（133 aa） Fragment：Alpha chain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 5000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.288

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BOTA_BOTJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 1–133 Author chain C； PDBConstruct 1–133； UniProt 1–133

BOTROCETIN BETA CHAIN

OrganismNot specified

UniProt P22030

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–125 Chain D； UniProt 1–125	Not recorded	BOTROCETIN ALPHA CHAIN × 2 （P22029） MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；PEG 4000, PEG 400 and MgCl2, pH 8.5. VAPOR DIFFUSION, HANGING DROP at 295 K	Resolution 1.80 Å R-free 0.218

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 1FVU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IJK The von Willebrand Factor mutant (I546V) A1 domain-botrocetin Complex Deposited 2001-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–125（125 aa） Fragment：b-subunit	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.279
1U0N The ternary von Willebrand Factor A1-glycoprotein Ibalpha-botrocetin complex Deposited 2004-07-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–125（125 aa） Fragment：Beta chain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；Sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.95 Å R-free 0.276
1U0O The mouse von Willebrand Factor A1-botrocetin complex Deposited 2004-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–125（125 aa） Fragment：Beta chain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 5000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.288

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BOTB_BOTJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–125； UniProt 1–125 Author chain D； PDBConstruct 1–125； UniProt 1–125

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	1fvu
Deposition date deposition_date	2000-09-20
Structure title title	CRYSTAL STRUCTURE OF BOTROCETIN
Keywords keywords	VON WILLBRAND FACTOR MODULATOR, C-TYPE LECTIN, METAL-BINDING, LOOP EXCHANGED DIMER, 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	25.69 Å
Radius of gyration Rg (electron density) rg_electron	24.28 Å
Forward intensity I(0) i0	59130300.00
Molecular weight molecular_weight	59140.0 kDa
Excluded volume excluded_volume	73395 Å³
Envelope volume envelope_volume	86681 Å³
Hydration-shell volume shell_volume	29689 Å³
Envelope diameter envelope_diameter	85.1 Å
Shell Rg shell_rg	31.69 Å
Envelope Rg envelope_rg	24.43 Å
Shape Rg shape_rg	24.26 Å
Total Rg total_rg	25.13 Å
Total atoms total_atoms	4162
Residues n_residues	508
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	81.7 Å
Rg (real space) rg_real	25.54 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	5.9130e+07
I(0) uncertainty (real space) i0_real_error	8.2070e+05
Rg (reciprocal space) rg_reciprocal	25.59 Å
I(0) (reciprocal space) i0_reciprocal	59130000.0000
Solution quality estimate total_estimate	0.8994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	80.3 Å
Skewness Skewness skewness	0.065
Kurtosis Kurtosis kurtosis	-0.603
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20440000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.991

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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	BOTROCETIN ALPHA CHAIN
Molecular weight formula_weight	15233.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4765

DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNIQSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYCAQKNPFVCKSPPP

Entity 2 Entity 2 polymer

Description description	BOTROCETIN BETA CHAIN
Molecular weight formula_weight	15050.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLKGDVVWIGLSDVWNKCRFEWTDGMEFDYDDYYLIAEYECVASKPTNNKWWIIPCTRFKNFVCEFQA

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	603

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1fvua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1fvub_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1fvuc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1fvud_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (4 domains)

Domain ID domain_id	1fvuA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1fvuB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1fvuC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1fvuD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (1)

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Unit-cell length a length_a	64.829 Å
Unit-cell length b length_b	69.666 Å
Unit-cell length c length_c	103.509 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1970
R_work r_work	0.1990
R_free r_free	0.2180

fit	/app/data/saxs_computation/fv/1fvu/1fvu.fit
pddf	/app/data/pr_computation/fv/1fvu/1fvu.pr.out
profile	/app/data/saxs_computation/fv/1fvu/1fvu.dat

CRYSTAL STRUCTURE OF BOTROCETIN

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

BOTROCETIN ALPHA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

BOTROCETIN BETA CHAIN

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)