SAXSdb — 1dbn

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Homooligomer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 2 PDB declaration: dimeric	Entity 1：PROTEIN (LEUKOAGGLUTININ) × 2 Entity 2：N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG 1000, PEG 8000, sialyllactose, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.75 Å R-free 0.253

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	1dbn
Deposition date deposition_date	1999-11-03
Structure title title	MAACKIA AMURENSIS LEUKOAGGLUTININ (LECTIN) WITH SIALYLLACTOSE
Keywords keywords	PLANT LECTIN, CARBOHYDRATE BINDING, SIALYLLACTOSE, SUGAR BINDING PROTEIN; SUGAR BINDING 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	25.15 Å
Radius of gyration Rg (electron density) rg_electron	23.87 Å
Forward intensity I(0) i0	47515400.00
Molecular weight molecular_weight	54372.0 kDa
Excluded volume excluded_volume	68176 Å³
Envelope volume envelope_volume	78114 Å³
Hydration-shell volume shell_volume	27211 Å³
Envelope diameter envelope_diameter	79.3 Å
Shell Rg shell_rg	31.14 Å
Envelope Rg envelope_rg	23.97 Å
Shape Rg shape_rg	23.84 Å
Total Rg total_rg	24.77 Å
Total atoms total_atoms	3844
Residues n_residues	478
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	78.0 Å
Rg (real space) rg_real	25.10 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	4.7520e+07
I(0) uncertainty (real space) i0_real_error	6.5860e+05
Rg (reciprocal space) rg_reciprocal	25.12 Å
I(0) (reciprocal space) i0_reciprocal	47520000.0000
Solution quality estimate total_estimate	0.9105
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.244
Kurtosis Kurtosis kurtosis	-0.581
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8402000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PROTEIN (LEUKOAGGLUTININ)
Molecular weight formula_weight	25987.6 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	3874

SDELSFTINNFVPNEADLLFQGEASVSSTGVLQLTKVENGQPQKYSVGRALYAAPVRIWGNTTGSVASFSTSFTFVVKAPNPDITSDGLAFYLAPPDSQIPSGSVSKYLGLFNNSNSDSSNQIVAVEFDTYFAHSYDPWDPNYRHIGIDVNGIESIKTVQWDWINGGVAFATITYLAPNKTLIASLVYPSNQTTFSVAASVDLKEILPEWVRVGFSAATGYPTEVETHDVLSWSFTSTL

Entity 2 Entity 2 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
Molecular weight formula_weight	633.6 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 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 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dbna_
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	d1dbnb_
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	1dbnA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1dbnB00
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 (3)

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Unit-cell length a length_a	80.742 Å
Unit-cell length b length_b	88.450 Å
Unit-cell length c length_c	84.496 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2240
R_work r_work	0.2210
R_free r_free	0.2530

fit	/app/data/saxs_computation/db/1dbn/1dbn.fit
pddf	/app/data/pr_computation/db/1dbn/1dbn.pr.out
profile	/app/data/saxs_computation/db/1dbn/1dbn.dat

MAACKIA AMURENSIS LEUKOAGGLUTININ (LECTIN) WITH SIALYLLACTOSE

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

Assembly Composition of the Current Entry

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