SAXSdb — 1dgl

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

LECTIN

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	Other combination Homooligomer Protein × 4 其他Polymer 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–237 Chain B； UniProt 1–237	Not recorded	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl alpha-D-mannopyranoside × 4 CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；pH 7.2	Resolution 2.40 Å R-free 0.252

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 1DGL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1VLN A TRICLINIC CRYSTAL FORM OF THE LECTIN CONCANAVALIN A Deposited 1996-04-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 30–148（119 aa） Chain B 30–148（119 aa） Chain C 30–148（119 aa） Chain D 30–148（119 aa）	Not recorded	MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.265
1VLN A TRICLINIC CRYSTAL FORM OF THE LECTIN CONCANAVALIN A Deposited 1996-04-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 30–148（119 aa） Chain F 30–148（119 aa） Chain G 30–148（119 aa） Chain H 30–148（119 aa）	Not recorded	MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.265
2GDF Crystal structure of Dioclea violacea seed lectin Deposited 2006-03-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–237（237 aa） Chain B 1–237（237 aa） Chain C 1–237（237 aa） Chain D 1–237（237 aa）	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10% PEG 8000, 10% PEG 1000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.258
2JE9 CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE Deposited 2007-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–237（237 aa） Chain B 1–237（237 aa） Chain C 1–237（237 aa） Chain D 1–237（237 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 XMM 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside × 4 SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 15% PEG 4000, 0.1M HEPES, PH 7.5 AND 0.1M LITHIUM SULFATE	Resolution 2.10 Å R-free 0.239
2JEC crystal structure of recombinant DiocleA grandiflora lectin mutant E123A-H131N-K132Q complexed witH 5-bromo-4-chloro-3-indolyl-a-D- mannose Deposited 2007-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–237（237 aa） Chain B 1–237（237 aa） Chain C 1–237（237 aa） Chain D 1–237（237 aa）	Mutation：YES Mutation：YES Mutation：YES Mutation：YES	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 8 XMM 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 18% PEG 8000, 0.1M CACODYLATE, PH 6.5 AND 0.2M ZINC ACETATE	Resolution 2.00 Å R-free 0.230
4Z8B crystal structure of a DGL mutant - H51G H131N Deposited 2015-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa）	Mutation：H51G;H131N	CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 4 GOL GLYCEROL × 2 XMM 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；RESERVOIR SOLUTION:100 mM HEPES, 14% polyethylene glycol 400 PROTEIN SOLUTION: 10 mM HEPES, 2 mM Cl2Ca, 2 mM Cl2Mn 3 mM X-Man (5-bromo-4-chloro-3-indolyl-ALPHA-D-mannose	Resolution 1.95 Å R-free 0.243

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LECA_DIOGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–237； UniProt 1–237 Author chain B； PDBConstruct 1–237； UniProt 1–237

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	1dgl
Deposition date deposition_date	1998-02-10
Structure title title	LECTIN FROM DIOCLEA GRANDIFLORA COMPLEXED TO TRIMANNOSIDE
Keywords keywords	LECTIN, SACCHARIDE BINDING, TRIMANNOSIDE; LECTIN
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	26.13 Å
Radius of gyration Rg (electron density) rg_electron	25.07 Å
Forward intensity I(0) i0	45898900.00
Molecular weight molecular_weight	52320.0 kDa
Excluded volume excluded_volume	65251 Å³
Envelope volume envelope_volume	75742 Å³
Hydration-shell volume shell_volume	26045 Å³
Envelope diameter envelope_diameter	87.9 Å
Shell Rg shell_rg	31.50 Å
Envelope Rg envelope_rg	25.14 Å
Shape Rg shape_rg	25.00 Å
Total Rg total_rg	25.98 Å
Total atoms total_atoms	3688
Residues n_residues	474
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	85.5 Å
Rg (real space) rg_real	26.24 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	4.5900e+07
I(0) uncertainty (real space) i0_real_error	6.9290e+05
Rg (reciprocal space) rg_reciprocal	26.21 Å
I(0) (reciprocal space) i0_reciprocal	45900000.0000
Solution quality estimate total_estimate	0.8807
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.447
Kurtosis Kurtosis kurtosis	-0.393
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7905000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.943

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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	LECTIN
Molecular weight formula_weight	25572.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3898

ADTIVAVELNSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFHQFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl alpha-D-mannopyranoside
Molecular weight formula_weight	518.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	190

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dgla_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

Domain ID domain_id	d1dglb_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

CATH v4.4 (2 domains)

Domain ID domain_id	1dglA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1dglB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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8. Citations (2)

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Unit-cell length a length_a	92.110 Å
Unit-cell length b length_b	92.110 Å
Unit-cell length c length_c	202.820 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2520

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

LECTIN FROM DIOCLEA GRANDIFLORA COMPLEXED TO TRIMANNOSIDE

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

LECTIN

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