SAXSdb — 1avb

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

ARCELIN-1

OrganismNot specified

UniProt P19329

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 × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 22–247 Chain B； UniProt 22–247	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.8；PROTEIN WAS CRYSTALLIZED FROM 25% PEG400, 0.3 M AMMONIUM SULFATE IN 0.1 M MES BUFFER PH 4.8-4.9	Resolution 1.90 Å R-free 0.242

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ARC1_PHAVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–226； UniProt 22–247 Author chain B； PDBConstruct 1–226； UniProt 22–247

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	1avb
Deposition date deposition_date	1997-09-15
Structure title title	ARCELIN-1 FROM PHASEOLUS VULGARIS L
Keywords keywords	LECTIN-LIKE GLYCOPROTEIN, PLANT DEFENSE, INSECTICIDAL ACTIVITY, LECTIN; 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	25.63 Å
Radius of gyration Rg (electron density) rg_electron	24.46 Å
Forward intensity I(0) i0	47690000.00
Molecular weight molecular_weight	51636.0 kDa
Excluded volume excluded_volume	63800 Å³
Envelope volume envelope_volume	76075 Å³
Hydration-shell volume shell_volume	26261 Å³
Envelope diameter envelope_diameter	85.7 Å
Shell Rg shell_rg	31.20 Å
Envelope Rg envelope_rg	24.61 Å
Shape Rg shape_rg	24.42 Å
Total Rg total_rg	25.35 Å
Total atoms total_atoms	3638
Residues n_residues	452
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	85.1 Å
Rg (real space) rg_real	25.67 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	4.7690e+07
I(0) uncertainty (real space) i0_real_error	5.9380e+05
Rg (reciprocal space) rg_reciprocal	25.66 Å
I(0) (reciprocal space) i0_reciprocal	47690000.0000
Solution quality estimate total_estimate	0.8858
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.5 Å
Skewness Skewness skewness	0.385
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6134000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.987

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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	ARCELIN-1
Molecular weight formula_weight	24984.6 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	3868

SNDASFNVETFNKTNLILQGDATVSSEGHLLLTNVKGNEEDSMGRAFYSAPIQINDRTIDNLASFSTNFTFRINAKNIENSAYGLAFALVPVGSRPKLKGRYLGLFNTTNYDRDAHTVAVVFDTVSNRIEIDVNSIRPIATESCNFGHNNGEKAEVRITYDSPKNDLRVSLLYPSSEEKCHVSATVPLEKEVEDWVSVGFSATSGSKKETTETHNVLSWSFSSNFI

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 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	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	230

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1avba_
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	d1avbb_
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	1avbA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1avbB00
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	85.650 Å
Unit-cell length b length_b	92.570 Å
Unit-cell length c length_c	67.280 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	1.900 Å
Low-resolution limit resolution_low	33.710 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2420

fit	/app/data/saxs_computation/av/1avb/1avb.fit
pddf	/app/data/pr_computation/av/1avb/1avb.pr.out
profile	/app/data/saxs_computation/av/1avb/1avb.dat

ARCELIN-1 FROM PHASEOLUS VULGARIS L

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

ARCELIN-1

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