← Back to search
1bry

BRYODIN TYPE I RIP

Method: X-RAY DIFFRACTION Dmax: 99.3 Å Quality: GOOD
▼

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

BRYODIN I

Bryonia dioica

UniProt P33185

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain Y； UniProt 24–270 Fragment：RESIDUES 1 - 247 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；0.1M MES (PH 6.0), 23% MEPEG5K, 0.2M AMMONIUM SULFATE, 0.1M LICL Resolution 2.10 Å R-free 0.298
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain Z； UniProt 24–270 Fragment：RESIDUES 1 - 247 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；0.1M MES (PH 6.0), 23% MEPEG5K, 0.2M AMMONIUM SULFATE, 0.1M LICL Resolution 2.10 Å R-free 0.298

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 RIP1_BRYDI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain Y； PDBConstruct 2–248； UniProt 24–270 Author chain Z； PDBConstruct 2–248； UniProt 24–270

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 1bry

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bry
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1bry
Deposition date deposition_date1997-02-14
Structure title titleBRYODIN TYPE I RIP
Keywords keywordsRIBOSOME-INACTIVATING PROTEIN, IMMUNOTOXIN, BRYODIN; RIBOSOME-INACTIVATING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier30.57 Å
Radius of gyration Rg (electron density) rg_electron29.95 Å
Forward intensity I(0) i045278400.00
Molecular weight molecular_weight54104.0 kDa
Excluded volume excluded_volume68398 ų
Envelope volume envelope_volume84961 ų
Hydration-shell volume shell_volume24920 ų
Envelope diameter envelope_diameter100.5 Å
Shell Rg shell_rg35.18 Å
Envelope Rg envelope_rg29.73 Å
Shape Rg shape_rg29.93 Å
Total Rg total_rg30.55 Å
Total atoms total_atoms3822
Residues n_residues494
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax99.3 Å
Rg (real space) rg_real30.77 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real4.5280e+07
I(0) uncertainty (real space) i0_real_error6.6810e+05
Rg (reciprocal space) rg_reciprocal30.69 Å
I(0) (reciprocal space) i0_reciprocal45280000.0000
Solution quality estimate total_estimate0.8262
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.8 Å
Skewness Skewness skewness0.379
Kurtosis Kurtosis kurtosis-0.744
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11600000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.720; Smooth: 0.817
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1bryy_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.1 — Plant cytotoxins
Domain ID domain_idd1bryz_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.1 — Plant cytotoxins

CATH v4.4 (4 domains)

Domain ID domain_id1bryY01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id1bryY02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2
Domain ID domain_id1bryZ01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id1bryZ02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2
▶

8. Citations (2)

▶

9. Files and Curves (10)