SAXSdb — 1bjq

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

LECTIN

Vigna unguiculata subsp. cylindrica

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 23–275 Chain B； UniProt 23–275 Chain C； UniProt 23–275 Chain D； UniProt 23–275	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 ADE ADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；100 MM NA-CACODYLATE PH 6.5 10 % (W/V) PEG 8000 20 MM MGAC2 1 MM ADENINE	Resolution 2.65 Å R-free 0.246
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 23–275 Chain F； UniProt 23–275 Chain G； UniProt 23–275 Chain H； UniProt 23–275	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 ADE ADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；100 MM NA-CACODYLATE PH 6.5 10 % (W/V) PEG 8000 20 MM MGAC2 1 MM ADENINE	Resolution 2.65 Å R-free 0.246

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 1BJQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LU1 THE STRUCTURE OF THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE FORSSMAN DISACCHARIDE Deposited 1998-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–275（253 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 ADE ADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；100 MM HEPES PH 7.5 0.2 M MGCL2 30% (W/V) PEG 400	Resolution 2.60 Å R-free 0.234
1LU2 DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE BLOOD GROUP A TRISACCHARIDE Deposited 1998-07-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–275（253 aa） Chain B 23–275（253 aa）	Not recorded	A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 4 CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.6；100 MM NACACO PH 6.6 15% (W/V) PEG-ME 5000 10 MM BLOOD GROUP A TRISACCHARIDE	Resolution 2.80 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	LEC1_DOLBI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 23–275 Author chain B； PDBConstruct 1–253； UniProt 23–275 Author chain C； PDBConstruct 1–253； UniProt 23–275 Author chain D； PDBConstruct 1–253； UniProt 23–275 Author chain E； PDBConstruct 1–253； UniProt 23–275 Author chain F； PDBConstruct 1–253； UniProt 23–275 Author chain G； PDBConstruct 1–253； UniProt 23–275 Author chain H； PDBConstruct 1–253； UniProt 23–275

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	1bjq
Deposition date deposition_date	1998-06-26
Structure title title	THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE
Keywords keywords	GLYCOPROTEIN, LECTIN, ADENINE, QUATERNARY STRUCTURE, LEGUME LECTIN; GLYCOPROTEIN
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	46.21 Å
Radius of gyration Rg (electron density) rg_electron	46.39 Å
Forward intensity I(0) i0	631910000.00
Molecular weight molecular_weight	208180.0 kDa
Excluded volume excluded_volume	260300 Å³
Envelope volume envelope_volume	326230 Å³
Hydration-shell volume shell_volume	62188 Å³
Envelope diameter envelope_diameter	158.5 Å
Shell Rg shell_rg	46.60 Å
Envelope Rg envelope_rg	46.19 Å
Shape Rg shape_rg	46.36 Å
Total Rg total_rg	46.51 Å
Total atoms total_atoms	14698
Residues n_residues	1940
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	151.9 Å
Rg (real space) rg_real	46.72 Å
Rg uncertainty (real space) rg_real_error	1.27 Å
I(0) (real space) i0_real	6.3190e+08
I(0) uncertainty (real space) i0_real_error	1.1620e+07
Rg (reciprocal space) rg_reciprocal	46.21 Å
I(0) (reciprocal space) i0_reciprocal	631500000.0000
Solution quality estimate total_estimate	0.7953
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.7 Å
Skewness Skewness skewness	0.588
Kurtosis Kurtosis kurtosis	-0.292
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	60360000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.032

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	LECTIN
Molecular weight formula_weight	27115.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	14698

ANIQSFSFKNFNSPSFILQGDATVSSGKLQLTKVKENGIPTPSSLGRAFYSSPIQIYDKSTGAVASWATSFTVKISAPSKASFADGIAFALVPVGSEPRRNGGYLGVFDSDVYNNSAQTVAVEFDTLSNSGWDPSMKHIGIDVNSIKSIATVSWDLANGENAEILITYNAATSLLVASLVHPSRRTSYILSERVDITNELPEYVSVGFSATTGLSEGYIETHDVLSWSFASKLPDDSTAEPLDLASYLVRNVL

来源 Source

来源生物 organism	Vigna unguiculata subsp. cylindrica
通用名 common_name	horse gram
NCBI Class编号 ncbi_taxonomy_id	3840
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	ADENINE
Molecular weight formula_weight	135.1 kDa
Source method src_method	syn
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1bjqa_
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	d1bjqb_
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	d1bjqc_
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	d1bjqd_
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	d1bjqe_
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	d1bjqf_
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	d1bjqg_
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	d1bjqh_
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 (8 domains)

Domain ID domain_id	1bjqA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1bjqB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1bjqC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1bjqD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1bjqE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1bjqF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1bjqG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1bjqH00
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	81.377 Å
Unit-cell length b length_b	116.135 Å
Unit-cell length c length_c	224.620 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2460

fit	/app/data/saxs_computation/bj/1bjq/1bjq.fit
pddf	/app/data/pr_computation/bj/1bjq/1bjq.pr.out
profile	/app/data/saxs_computation/bj/1bjq/1bjq.dat

THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE

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