1dlp

STRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN SCILLA CAMPANULATA AGGLUTININ (SCAFET): A NOVEL TWO-DOMAIN LECTIN

Method: X-RAY DIFFRACTION D_max: 110.9 Å Quality: GOOD

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

LECTIN SCAFET PRECURSOR

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 22–257 Chain B； UniProt 22–257 Chain C； UniProt 22–257 Chain D； UniProt 22–257 Chain E； UniProt 22–257 Chain F； UniProt 22–257	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；70% Ammonium sulphate, Acetic Acid buffer, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.30 Å R-free 0.293

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	Q9ZP48_HYAHI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–236； UniProt 22–257 Author chain B； PDBConstruct 1–236； UniProt 22–257 Author chain C； PDBConstruct 1–236； UniProt 22–257 Author chain D； PDBConstruct 1–236； UniProt 22–257 Author chain E； PDBConstruct 1–236； UniProt 22–257 Author chain F； PDBConstruct 1–236； UniProt 22–257

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dlp
Deposition date deposition_date	1999-12-11
Structure title title	STRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN SCILLA CAMPANULATA AGGLUTININ (SCAFET): A NOVEL TWO-DOMAIN LECTIN
Keywords keywords	TWO-DOMAIN LECTIN, BETA PRISM II FOLD, NATIVE, 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	39.99 Å
Radius of gyration Rg (electron density) rg_electron	39.08 Å
Forward intensity I(0) i0	352988000.00
Molecular weight molecular_weight	147250.0 kDa
Excluded volume excluded_volume	181790 Å³
Envelope volume envelope_volume	257170 Å³
Hydration-shell volume shell_volume	53493 Å³
Envelope diameter envelope_diameter	108.8 Å
Shell Rg shell_rg	47.75 Å
Envelope Rg envelope_rg	36.58 Å
Shape Rg shape_rg	39.06 Å
Total Rg total_rg	39.63 Å
Total atoms total_atoms	10364
Residues n_residues	1358
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	110.9 Å
Rg (real space) rg_real	39.64 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	3.5300e+08
I(0) uncertainty (real space) i0_real_error	4.9760e+06
Rg (reciprocal space) rg_reciprocal	39.86 Å
I(0) (reciprocal space) i0_reciprocal	353100000.0000
Solution quality estimate total_estimate	0.8921
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	63.8 Å
Skewness Skewness skewness	-0.128
Kurtosis Kurtosis kurtosis	-0.912
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	47580000.0000
Real-space data points n_real_points	41
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: 1.000; Smooth: 0.749

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1dlpa1
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	d1dlpa2
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	d1dlpb1
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	d1dlpb2
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	d1dlpc1
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	d1dlpc2
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	d1dlpd1
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	d1dlpd2
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	d1dlpe1
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	d1dlpe2
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	d1dlpf1
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	d1dlpf2
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 (12 domains)

Domain ID domain_id	1dlpA01
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	1dlpA02
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	1dlpB01
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	1dlpB02
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	1dlpC01
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	1dlpC02
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	1dlpD01
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	1dlpD02
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	1dlpE01
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	1dlpE02
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	1dlpF01
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	1dlpF02
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	277.940 Å
Unit-cell length b length_b	164.100 Å
Unit-cell length c length_c	53.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1890
R_free r_free	0.2930

Description description	LECTIN SCAFET PRECURSOR
Molecular weight formula_weight	25545.4 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	10431

STRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN SCILLA CAMPANULATA AGGLUTININ (SCAFET): A NOVEL TWO-DOMAIN LECTIN

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

LECTIN SCAFET PRECURSOR

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

fit	/app/data/saxs_computation/dl/1dlp/1dlp.fit
pddf	/app/data/pr_computation/dl/1dlp/1dlp.pr.out
profile	/app/data/saxs_computation/dl/1dlp/1dlp.dat