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6v7j

The C2221 crystal form of canavalin at 173 K

Method: X-RAY DIFFRACTION Dmax: 104.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Canavalin

Canavalia ensiformis

UniProt P50477

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–445 Chain B； UniProt 1–445 Chain C； UniProt 1–445 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

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 6V7J 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
1DGR Refined crystal structure of canavalin from jack bean Deposited 1999-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 B 46–223（178 aa） Fragment：RESIDUES 46-223
Chain C 46–223（178 aa） Fragment：RESIDUES 46-223
Chain M 331–423（93 aa） Fragment：RESIDUES 331-423
Chain N 246–324（79 aa） Fragment：RESIDUES 246-324
Chain V 246–324（79 aa） Fragment：RESIDUES 246-324
Chain W 331–423（93 aa） Fragment：RESIDUES 331-423
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 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
1DGW Structure of the rhombohedral crystal of canavalin from jack bean Deposited 1999-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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 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 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
6V7L The structure of the P212121 crystal form of canavalin at 173 K Deposited 2019-12-08 Different mutation/modification 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
Chains and sequence ranges Author chain A； PDBConstruct 1–445； UniProt 1–445 Author chain B； PDBConstruct 1–445； UniProt 1–445 Author chain C； PDBConstruct 1–445； UniProt 1–445

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6v7j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6v7j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6v7j
Deposition date deposition_date2019-12-08
Structure title titleThe C2221 crystal form of canavalin at 173 K
Keywords keywordsplant protein, storage protein, trimer, benzoic acid, enzyme; PLANT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.84 Å
Radius of gyration Rg (electron density) rg_electron32.67 Å
Forward intensity I(0) i0225879000.00
Molecular weight molecular_weight121140.0 kDa
Excluded volume excluded_volume151740 ų
Envelope volume envelope_volume186270 ų
Hydration-shell volume shell_volume46380 ų
Envelope diameter envelope_diameter104.0 Å
Shell Rg shell_rg40.69 Å
Envelope Rg envelope_rg32.39 Å
Shape Rg shape_rg32.66 Å
Total Rg total_rg33.31 Å
Total atoms total_atoms8544
Residues n_residues1052
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.9 Å
Rg (real space) rg_real33.75 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real2.2590e+08
I(0) uncertainty (real space) i0_real_error3.3790e+06
Rg (reciprocal space) rg_reciprocal33.81 Å
I(0) (reciprocal space) i0_reciprocal225900000.0000
Solution quality estimate total_estimate0.9102
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.7 Å
Skewness Skewness skewness0.176
Kurtosis Kurtosis kurtosis-0.672
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha144600000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.965
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6v7ja1
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.1 — RmlC-like cupins
Family Family familyb.82.1.2 — Germin/Seed storage 7S protein
Domain ID domain_idd6v7ja2
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.1 — RmlC-like cupins
Family Family familyb.82.1.2 — Germin/Seed storage 7S protein
Domain ID domain_idd6v7jb1
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.1 — RmlC-like cupins
Family Family familyb.82.1.2 — Germin/Seed storage 7S protein
Domain ID domain_idd6v7jb2
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.1 — RmlC-like cupins
Family Family familyb.82.1.2 — Germin/Seed storage 7S protein
Domain ID domain_idd6v7jc1
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.1 — RmlC-like cupins
Family Family familyb.82.1.2 — Germin/Seed storage 7S protein
Domain ID domain_idd6v7jc2
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.1 — RmlC-like cupins
Family Family familyb.82.1.2 — Germin/Seed storage 7S protein
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8. Citations (1)

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9. Files and Curves (10)