SAXSdb — 1kj1

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

lectin I

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	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 177–284	Not recorded	lectin II × 1 （Q38783） MAN alpha-D-mannopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% PEG 8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS, 1WEEK, pH 7.00, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.20 Å R-free 0.251
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain P； UniProt 177–284	Not recorded	lectin II × 1 （Q38783） MAN alpha-D-mannopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% PEG 8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS, 1WEEK, pH 7.00, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.20 Å R-free 0.251

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 1KJ1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BWU MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE Deposited 1998-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 177–282（106 aa） Chain P 18–123（106 aa）	Not recorded	MAN alpha-D-mannopyranose × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；20% PEG8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS PH 7.0, 1 WEEK, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278
1BWU MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE Deposited 1998-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 18–123（106 aa）	Not recorded	MAN alpha-D-mannopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；20% PEG8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS PH 7.0, 1 WEEK, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278
1BWU MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE Deposited 1998-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 177–282（106 aa）	Not recorded	MAN alpha-D-mannopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；20% PEG8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS PH 7.0, 1 WEEK, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q38789_ALLSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 177–284 Author chain P； PDBConstruct 1–109； UniProt 177–284

lectin II

OrganismNot specified

UniProt Q38783

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 29–137	Not recorded	lectin I × 1 （Q38789） MAN alpha-D-mannopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% PEG 8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS, 1WEEK, pH 7.00, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.20 Å R-free 0.251
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Q； UniProt 29–137	Not recorded	lectin I × 1 （Q38789） MAN alpha-D-mannopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% PEG 8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS, 1WEEK, pH 7.00, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.20 Å R-free 0.251

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	Q38783_ALLSA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–109； UniProt 29–137 Author chain Q； PDBConstruct 1–109； UniProt 29–137

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	1kj1
Deposition date deposition_date	2001-12-04
Structure title title	MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE
Keywords keywords	BULB LECTIN, MANNOSE, PLANT PROTEIN; PLANT 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	27.10 Å
Radius of gyration Rg (electron density) rg_electron	26.29 Å
Forward intensity I(0) i0	45634700.00
Molecular weight molecular_weight	50774.0 kDa
Excluded volume excluded_volume	62688 Å³
Envelope volume envelope_volume	77031 Å³
Hydration-shell volume shell_volume	25139 Å³
Envelope diameter envelope_diameter	89.1 Å
Shell Rg shell_rg	32.57 Å
Envelope Rg envelope_rg	25.97 Å
Shape Rg shape_rg	26.25 Å
Total Rg total_rg	27.05 Å
Total atoms total_atoms	3570
Residues n_residues	436
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	87.4 Å
Rg (real space) rg_real	27.08 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	4.5630e+07
I(0) uncertainty (real space) i0_real_error	6.6650e+05
Rg (reciprocal space) rg_reciprocal	27.09 Å
I(0) (reciprocal space) i0_reciprocal	45630000.0000
Solution quality estimate total_estimate	0.9040
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.255
Kurtosis Kurtosis kurtosis	-0.539
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6088000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.981

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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 I
Molecular weight formula_weight	11988.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,P
Atom count atom_count	3745

RNLLTNGEGLYAGQSLDVEPYHFIMQEDCNLVLYDHSTSVWASNTGILGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTGTYK

Entity 2 Entity 2 polymer

Description description	lectin II
Molecular weight formula_weight	12169.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,Q

RNILMNDEGLYAGQSLDVEPYHLIMQEDCNLVLYDHSTAVWTTNTDIPGKKGCKAVLQSDGNFVVYDAEGRSLWASHSVRGNGNYVLVLQEDGNVVIYGSDIWSTNTYK

Entity 3 Entity 3 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	14

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	175

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1kj1a_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

Domain ID domain_id	d1kj1d_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

Domain ID domain_id	d1kj1p_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

Domain ID domain_id	d1kj1q_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

CATH v4.4 (4 domains)

Domain ID domain_id	1kj1A00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	1kj1D00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	1kj1P00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	1kj1Q00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

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8. Citations (3)

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Unit-cell length a length_a	201.831 Å
Unit-cell length b length_b	43.516 Å
Unit-cell length c length_c	78.736 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2510

fit	/app/data/saxs_computation/kj/1kj1/1kj1.fit
pddf	/app/data/pr_computation/kj/1kj1/1kj1.pr.out
profile	/app/data/saxs_computation/kj/1kj1/1kj1.dat

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE

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

lectin I

State in the Current Structure

Other States of the Same Protein in the Database

lectin II

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)