1b2p

NATIVE MANNOSE-SPECIFIC BULB LECTIN FROM SCILLA CAMPANULATA (BLUEBELL) AT 1.7 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 66.4 Å Quality: GOOD

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

PROTEIN (LECTIN)

OrganismNot specified

UniProt Q9ZP49

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 22–140 Chain B; UniProt 22–140 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.7;HANGING-DROP VAPOUR-DIFFUSION METHOD WELL: 70% SATURATED AMMONIUM SULPHATE, PH 4.7 DROP: 5.5 MG/ML PROTEIN, 10MM DAP, 600MM PHOSPHATE BUFFERED SALINE, VAPOR DIFFUSION, HANGING DROP Resolution 1.70 Å R-free 0.208
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 22–140 Chain B; UniProt 22–140 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.7;HANGING-DROP VAPOUR-DIFFUSION METHOD WELL: 70% SATURATED AMMONIUM SULPHATE, PH 4.7 DROP: 5.5 MG/ML PROTEIN, 10MM DAP, 600MM PHOSPHATE BUFFERED SALINE, VAPOR DIFFUSION, HANGING DROP Resolution 1.70 Å R-free 0.208

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 Q9ZP49_HYAHI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–119; UniProt 22–140 Author chain B; PDBConstruct 1–119; UniProt 22–140

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 1b2p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b2p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b2p
Deposition date deposition_date1998-11-30
Structure title titleNATIVE MANNOSE-SPECIFIC BULB LECTIN FROM SCILLA CAMPANULATA (BLUEBELL) AT 1.7 ANGSTROMS RESOLUTION
Keywords keywordsMANNOSE-BINDING LECTIN, MONOCOT, AGLUTININ, BLUEBELL BULBS, PROTEIN- CARBOHYDRATE INTERACTIONS, 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_guinier19.73
Radius of gyration Rg (electron density) rg_electron18.43
Forward intensity I(0) i012470500.00
Molecular weight molecular_weight26392.0 kDa
Excluded volume excluded_volume32986 ų
Envelope volume envelope_volume37262 ų
Hydration-shell volume shell_volume17367 ų
Envelope diameter envelope_diameter69.0
Shell Rg shell_rg24.32
Envelope Rg envelope_rg18.67
Shape Rg shape_rg18.39
Total Rg total_rg19.44
Total atoms total_atoms1864
Residues n_residues238
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 dmax66.4
Rg (real space) rg_real19.72
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real1.2470e+07
I(0) uncertainty (real space) i0_real_error1.5770e+05
Rg (reciprocal space) rg_reciprocal19.72
I(0) (reciprocal space) i0_reciprocal12470000.0000
Solution quality estimate total_estimate0.8023
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.3
Skewness Skewness skewness0.350
Kurtosis Kurtosis kurtosis-0.186
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1756000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1b2pa_
Class classb — All beta proteins
Fold Fold foldb.78 — beta-Prism II
Superfamily Superfamily superfamilyb.78.1 — alpha-D-mannose-specific plant lectins
Family Family familyb.78.1.1 — alpha-D-mannose-specific plant lectins
Domain ID domain_idd1b2pb_
Class classb — All beta proteins
Fold Fold foldb.78 — beta-Prism II
Superfamily Superfamily superfamilyb.78.1 — alpha-D-mannose-specific plant lectins
Family Family familyb.78.1.1 — alpha-D-mannose-specific plant lectins

CATH v4.4 (2 domains)

Domain ID domain_id1b2pA00
Class class2 — Mainly Beta
Architecture architecture90 — Orthogonal Prism
Topology topology10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily10 — Bulb-type lectin domain
Domain ID domain_id1b2pB00
Class class2 — Mainly Beta
Architecture architecture90 — Orthogonal Prism
Topology topology10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily10 — Bulb-type lectin domain

8. Citations (5)

9. Files and Curves (10)