1c3k

CRYSTAL STRUCTURE OF HELIANTHUS TUBEROSUS LECTIN

Method: X-RAY DIFFRACTION Dmax: 51.5 Å Quality: REASONABLE

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

AGGLUTININ

OrganismNot specified

UniProt Q9ZQY5

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 1–147 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7;298 K;26-28% PEG MONOMETHYL ESTER 550, 0.2 M MAGNESIUM ACETATE, pH 7.0, VAPOR DIFFUSION, temperature 298K Resolution 2.00 Å R-free 0.255
2 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1–147 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7;298 K;26-28% PEG MONOMETHYL ESTER 550, 0.2 M MAGNESIUM ACETATE, pH 7.0, VAPOR DIFFUSION, temperature 298K Resolution 2.00 Å R-free 0.255

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 Q9ZQY5_HELTU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–147; UniProt 1–147

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

SAXS profile for 1c3k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c3k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1c3k
Deposition date deposition_date1999-07-28
Structure title titleCRYSTAL STRUCTURE OF HELIANTHUS TUBEROSUS LECTIN
Keywords keywordsBETA PRISM, AGGLUTININ, JACALIN-RELATED, MANNOSE, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.51
Radius of gyration Rg (electron density) rg_electron14.13
Forward intensity I(0) i04205420.00
Molecular weight molecular_weight15126.0 kDa
Excluded volume excluded_volume19133 ų
Envelope volume envelope_volume20984 ų
Hydration-shell volume shell_volume12606 ų
Envelope diameter envelope_diameter53.1
Shell Rg shell_rg20.03
Envelope Rg envelope_rg14.56
Shape Rg shape_rg14.09
Total Rg total_rg15.46
Total atoms total_atoms1071
Residues n_residues143
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax51.5
Rg (real space) rg_real15.43
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real4.2050e+06
I(0) uncertainty (real space) i0_real_error5.1900e+04
Rg (reciprocal space) rg_reciprocal15.44
I(0) (reciprocal space) i0_reciprocal4205000.0000
Solution quality estimate total_estimate0.6181
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.2
Skewness Skewness skewness0.201
Kurtosis Kurtosis kurtosis-0.199
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha758300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.755; Stabil: 0.999; Sysdev: 0.256; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1c3ka_
Class classb — All beta proteins
Fold Fold foldb.77 — beta-Prism I
Superfamily Superfamily superfamilyb.77.3 — Mannose-binding lectins
Family Family familyb.77.3.1 — Mannose-binding lectins

CATH v4.4 (1 domains)

Domain ID domain_id1c3kA00
Class class2 — Mainly Beta
Architecture architecture100 — Aligned Prism
Topology topology10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily30 — Jacalin-like lectin domain

8. Citations (1)

9. Files and Curves (10)