SAXSdb — 1dgr

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

CANAVALIN

OrganismNot specified

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 homooligomer Homooligomer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 46–223 Chain B； UniProt 46–223 Chain C； UniProt 46–223 Chain M； UniProt 331–423 Chain N； UniProt 246–324 Chain V； UniProt 246–324 Chain W； UniProt 331–423 Chain X； UniProt 246–324 Chain Y； UniProt 331–423	Fragment：RESIDUES 46-223 Fragment：RESIDUES 246-324 Fragment：RESIDUES 331-423	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；Dulbeccos phosphate buffered saline, ammonium hydroxide, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.226

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 1DGR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CAU DETERMINATION OF THREE CRYSTAL STRUCTURES OF CANAVALIN BY MOLECULAR REPLACEMENT Deposited 1993-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 44–224（181 aa） Chain B 241–424（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1CAV THE THREE-DIMENSIONAL STRUCTURE OF CANAVALIN FROM JACK BEAN (CANAVALIA ENSIFORMIS) Deposited 1993-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 44–224（181 aa） Chain B 241–424（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1CAW DETERMINATION OF THREE CRYSTAL STRUCTURES OF CANAVALIN BY MOLECULAR REPLACEMENT Deposited 1993-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 44–224（181 aa） Chain B 241–424（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1CAX DETERMINATION OF THREE CRYSTAL STRUCTURES OF CANAVALIN BY MOLECULAR REPLACEMENT Deposited 1993-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 44–224（181 aa） Chain B 241–424（184 aa） Chain C 44–224（181 aa） Chain D 241–424（184 aa） Chain E 44–224（181 aa） Chain F 241–424（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1DGW Structure of the rhombohedral crystal of canavalin from jack bean Deposited 1999-11-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric	Chain A 46–223（178 aa） Fragment：RESIDUES 46-223 Chain X 246–324（79 aa） Fragment：RESIDUES 246-324 Chain Y 331–423（93 aa） Fragment：RESIDUES 331-423	Not recorded	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 6.8；293 K；DULBECCO'S PHOSPHATE BUFFERED SALINE, AMMONIUM HYDROXIDE (TRACE), MICROGRAVITY, pH 6.8, LIQUID DIFFUSION, temperature 293K	Resolution 1.70 Å R-free 0.252
2CAU CANAVALIN FROM JACK BEAN Deposited 1998-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–445（445 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；THIS CRYSTAL FORM COULD BE GROWN ONLY OCCASIONALLY. BASICALLY IT WAS CRYSTALLIZED FROM PURIFIED PROTEIN AFTER TRYPSIN TREATMENT IN PHOSPHATE BUFFERED SALINE, BUT WAS DIFFICULT TO REPRODUCE., pH 6.8	Resolution 2.10 Å R-free 0.235
2CAV CANAVALIN FROM JACK BEAN Deposited 1998-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–445（445 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；30 - 40 MG/ML PROTEIN SOLUTION WAS PREPARED BY DISSOLVING 4-TIME RECRYSTALLIZED CANAVALIN IN DISTILLED WATER PLUS TRACE NH4OH. RESERVOIR SOLUTION CONTAINED 2.0 % NACL IN 50 MM PHOSPHATE BUFFER AT PH 6.8. CRYSTALS WERE OBTAINED BY MIXING PROTEIN AND RESERVOIR SOLUTION IN SITTING DROPS FOLLOWED BY VAPOR DIFFUSION AGAINST THE RESERVOIR., vapor diffusion	Resolution 2.00 Å R-free 0.264
6V7G Binding of Benzoic Acid and Anions Within the Cupin Domains of the Vicillin Protein Canavalin from Jack Bean (canavalia ensiformis): Crystal Structures Deposited 2019-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–445（445 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 3 BEZ BENZOIC ACID × 3 CIT CITRIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；Vapor diffusion in sitting drop Cryschem plates. Reservoirs were 1.0 M sodium citrate titrated with acetic acid to pH6.0. Drops were initially equal amounts of the reservoir solution with a protein stock solution of 30 mg/ml canavalin in water with a trace of ammonium hydroxide. At room temperature crystallization time was about three weeks.	Resolution 1.40 Å R-free 0.188
6V7J The C2221 crystal form of canavalin at 173 K Deposited 2019-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–445（445 aa） Chain B 1–445（445 aa） Chain C 1–445（445 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	BEZ BENZOIC ACID × 3 GOL GLYCEROL × 3 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；Vapor diffusion in Cryschem sitting drop plates at room temperature. Reservoirs were Dulbeccos Phosphate buffered saline at pH 6.5. Drops were equal amounts of the reservoir and a 40 mg/ml solution of the protein dissolved in water with a trace of ammonium hydroxide. Crystallization time was 24 to 48 hours.	Resolution 2.00 Å R-free 0.247
6V7L The structure of the P212121 crystal form of canavalin at 173 K Deposited 2019-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–445（445 aa） Chain B 1–445（445 aa） Chain C 1–445（445 aa）	Not recorded	BEZ BENZOIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；Crystals were grown by sitting drop vapor diffusion from 18% PEG 3350 in 0.1 M HEPES reservoirs. The drops were equal amounts of a 40 mg/ml solution of precanavalin (not treated with any exogenous protease) in water. Crystals grew only after six to eight weeks at room temperature.	Resolution 2.80 Å R-free 0.252

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CANA_CANEN
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–178； UniProt 46–223 Author chain B； PDBConstruct 1–178； UniProt 46–223 Author chain C； PDBConstruct 1–178； UniProt 46–223 Author chain N； PDBConstruct 1–79； UniProt 246–324 Author chain V； PDBConstruct 1–79； UniProt 246–324 Author chain X； PDBConstruct 1–79； UniProt 246–324 Author chain M； PDBConstruct 1–93； UniProt 331–423 Author chain W； PDBConstruct 1–93； UniProt 331–423 Author chain Y； PDBConstruct 1–93； UniProt 331–423

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	1dgr
Deposition date deposition_date	1999-11-25
Structure title title	Refined crystal structure of canavalin from jack bean
Keywords keywords	DUPLICATED DOMAINS BETA BARREL HELICAL LOOP, PLANT PROTEIN; PLANT 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	33.74 Å
Radius of gyration Rg (electron density) rg_electron	32.59 Å
Forward intensity I(0) i0	217135000.00
Molecular weight molecular_weight	118510.0 kDa
Excluded volume excluded_volume	148400 Å³
Envelope volume envelope_volume	182540 Å³
Hydration-shell volume shell_volume	45711 Å³
Envelope diameter envelope_diameter	101.4 Å
Shell Rg shell_rg	40.41 Å
Envelope Rg envelope_rg	32.23 Å
Shape Rg shape_rg	32.59 Å
Total Rg total_rg	33.18 Å
Total atoms total_atoms	8362
Residues n_residues	1039
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	103.5 Å
Rg (real space) rg_real	33.65 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	2.1710e+08
I(0) uncertainty (real space) i0_real_error	3.4620e+06
Rg (reciprocal space) rg_reciprocal	33.71 Å
I(0) (reciprocal space) i0_reciprocal	217100000.0000
Solution quality estimate total_estimate	0.9086
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.175
Kurtosis Kurtosis kurtosis	-0.677
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	151900000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.917

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	CANAVALIN
Molecular weight formula_weight	20640.3 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8530

NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP

Entity 2 Entity 2 polymer

Description description	CANAVALIN
Molecular weight formula_weight	9073.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,V,N

DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLEQQQ

Entity 3 Entity 3 polymer

Description description	CANAVALIN
Molecular weight formula_weight	10269.4 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,W,M

MQLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQP

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	168

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7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1dgr.1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgr.2
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgr.4
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgra_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgrb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgrc_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

CATH v4.4 (9 domains)

Domain ID domain_id	1dgrA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1dgrB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1dgrC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1dgrM01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	840 —

Domain ID domain_id	1dgrN00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1450 —

Domain ID domain_id	1dgrV00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1450 —

Domain ID domain_id	1dgrW01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	840 —

Domain ID domain_id	1dgrX00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1450 —

Domain ID domain_id	1dgrY01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	840 —

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8. Citations (2)

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Unit-cell length a length_a	136.500 Å
Unit-cell length b length_b	150.300 Å
Unit-cell length c length_c	133.400 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	200.000 Å
R factor r_factor	0.1840
R_work r_work	0.1800
R_free r_free	0.2260

fit	/app/data/saxs_computation/dg/1dgr/1dgr.fit
pddf	/app/data/pr_computation/dg/1dgr/1dgr.pr.out
profile	/app/data/saxs_computation/dg/1dgr/1dgr.dat

Refined crystal structure of canavalin from jack bean

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

CANAVALIN

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)