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6caf

High Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), A Chitinase-like Protein

Method: X-RAY DIFFRACTION Dmax: 61.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Concanavalin B

Canavalia ensiformis

UniProt P49347

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–324 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；2% saturated ammonium sulfate buffered with Na phosphate at pH 6.5. Room temperature, crystallization in about 1 week. Protein dissolved in 5% NaCl and 0.1 M acetic acid. Resolution 1.30 Å R-free 0.128

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 6CAF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CNV CRYSTAL STRUCTURE OF CONCANAVALIN B AT 1.65 A RESOLUTION Deposited 1995-02-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–324（299 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.65 Å
6GWA Concanavalin B structure determined with data from the EuXFEL, the first MHz free electron laser Deposited 2018-06-22 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–324（299 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；293 K；Batch mode, acetone
Resolution 2.10 Å R-free 0.219

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CONB_CANEN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–324； UniProt 1–324

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 6caf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6caf
Deposition date deposition_date2018-01-30
Structure title titleHigh Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), A Chitinase-like Protein
Keywords keywordsSEED PROTEIN, chitinase-like protein, MES, Jack Bean, PLANT PROTEIN; 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_guinier19.63 Å
Radius of gyration Rg (electron density) rg_electron18.22 Å
Forward intensity I(0) i017981300.00
Molecular weight molecular_weight32562.0 kDa
Excluded volume excluded_volume40848 ų
Envelope volume envelope_volume45559 ų
Hydration-shell volume shell_volume20369 ų
Envelope diameter envelope_diameter65.0 Å
Shell Rg shell_rg25.01 Å
Envelope Rg envelope_rg18.55 Å
Shape Rg shape_rg18.16 Å
Total Rg total_rg19.32 Å
Total atoms total_atoms2298
Residues n_residues288
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 dmax61.8 Å
Rg (real space) rg_real19.48 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real1.7980e+07
I(0) uncertainty (real space) i0_real_error2.3360e+05
Rg (reciprocal space) rg_reciprocal19.50 Å
I(0) (reciprocal space) i0_reciprocal17980000.0000
Solution quality estimate total_estimate0.8909
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.2 Å
Skewness Skewness skewness0.119
Kurtosis Kurtosis kurtosis-0.418
Angular range angular_range— – 0.4050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2948000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.947
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6cafa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.5 — Type II chitinase

CATH v4.4 (1 domains)

Domain ID domain_id6cafA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
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8. Citations (1)

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9. Files and Curves (10)