← Back to search
1aqz

CRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RESTRICTOCIN

Method: X-RAY DIFFRACTION Dmax: 83.5 Å Quality: GOOD
▼

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

RESTRICTOCIN

OrganismNot specified

UniProt P67876

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 A； UniProt 28–176 Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：vapor diffusion and microdialysis；pH 6.8；A COMBINATION OF VAPOR DIFFUSION AND MICRODIALYSIS TECHNIQUES WERE USED TO CRYSTALLIZE RESTRICTOCIN. THE FINAL MOTHER LIQUOR CONSISTS OF 60% ETHANOL, 10MM SODIUM PHOSPHATE, PH6.8. THE PROTEIN CONCENTRATION IS 10MG/ML., vapor diffusion and microdialysis Resolution 1.70 Å R-free 0.177
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 28–176 Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：vapor diffusion and microdialysis；pH 6.8；A COMBINATION OF VAPOR DIFFUSION AND MICRODIALYSIS TECHNIQUES WERE USED TO CRYSTALLIZE RESTRICTOCIN. THE FINAL MOTHER LIQUOR CONSISTS OF 60% ETHANOL, 10MM SODIUM PHOSPHATE, PH6.8. THE PROTEIN CONCENTRATION IS 10MG/ML., vapor diffusion and microdialysis Resolution 1.70 Å R-free 0.177

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 1AQZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JBR Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor Deposited 2001-06-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 28–176（149 aa）
Not recorded K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG5000, K-MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.15 Å R-free 0.290
1JBR Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor Deposited 2001-06-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 28–176（149 aa）
Not recorded K POTASSIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG5000, K-MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.15 Å R-free 0.290
1JBT CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG Deposited 2001-06-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 28–176（149 aa）
Not recorded K POTASSIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG5000, K.MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.282
1JBT CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG Deposited 2001-06-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 28–176（149 aa）
Not recorded K POTASSIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG5000, K.MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.282

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNMG_ASPRE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–149； UniProt 28–176 Author chain B； PDBConstruct 1–149； UniProt 28–176

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 1aqz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1aqz
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1aqz
Deposition date deposition_date1997-08-04
Structure title titleCRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RESTRICTOCIN
Keywords keywordsRIBOTOXIN, RIBOSOME-INACTIVATING PROTEIN, PROTEIN-RNA SPECIFIC INTERACTION, LAUE DIFFRACTION, CELL-ENTRY ACTIVITY; RIBOTOXIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier23.50 Å
Radius of gyration Rg (electron density) rg_electron23.04 Å
Forward intensity I(0) i020265100.00
Molecular weight molecular_weight32461.0 kDa
Excluded volume excluded_volume39812 ų
Envelope volume envelope_volume48999 ų
Hydration-shell volume shell_volume18692 ų
Envelope diameter envelope_diameter85.1 Å
Shell Rg shell_rg28.37 Å
Envelope Rg envelope_rg23.07 Å
Shape Rg shape_rg23.01 Å
Total Rg total_rg23.77 Å
Total atoms total_atoms2287
Residues n_residues285
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 dmax83.5 Å
Rg (real space) rg_real23.60 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real2.0270e+07
I(0) uncertainty (real space) i0_real_error3.1100e+05
Rg (reciprocal space) rg_reciprocal23.58 Å
I(0) (reciprocal space) i0_reciprocal20260000.0000
Solution quality estimate total_estimate0.8460
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1 Å
Skewness Skewness skewness0.409
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2970000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.960
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1aqza_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.3 — Ribotoxin
Domain ID domain_idd1aqzb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.3 — Ribotoxin

CATH v4.4 (2 domains)

Domain ID domain_id1aqzA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1aqzB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
▶

8. Citations (6)

▶

9. Files and Curves (10)