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1de3

SOLUTION STRUCTURE OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN

Method: SOLUTION NMR Dmax: 53.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBONUCLEASE ALPHA-SARCIN

Aspergillus giganteus

UniProt P00655

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 28–177 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；308 K；Pressure AMBIENT NMR measurement conditions：pH 4；313 K；Pressure AMBIENT NMR sample composition：NA NMR sample composition：NA NMR sample composition：U-15N Resolution not provided

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 1DE3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1R4Y SOLUTION STRUCTURE OF THE DELETION MUTANT DELTA(7-22) OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN Deposited 2003-10-09 Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–177（150 aa）
Mutation：L7G, R22G, DEL(8-21) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；308 K；Pressure AMBIENT
NMR sample composition 2mM Ribonuclease; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 2mM Ribonuclease; D2O | D2O
Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNAS_ASPGI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–150； UniProt 28–177

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 1de3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1de3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1de3
Deposition date deposition_date1999-11-12
Structure title titleSOLUTION STRUCTURE OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN
Keywords keywordsALPHA-BETA PROTEIN, HYDROLASE; HYDROLASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.51 Å
Radius of gyration Rg (electron density) rg_electron15.53 Å
Forward intensity I(0) i01690530000.00
Molecular weight molecular_weight339760.0 kDa
Excluded volume excluded_volume420690 ų
Envelope volume envelope_volume34427 ų
Hydration-shell volume shell_volume16729 ų
Envelope diameter envelope_diameter64.0 Å
Shell Rg shell_rg23.43 Å
Envelope Rg envelope_rg17.90 Å
Shape Rg shape_rg15.45 Å
Total Rg total_rg15.88 Å
Total atoms total_atoms47100
Residues n_residues3000
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax53.5 Å
Rg (real space) rg_real15.47 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real1.6910e+09
I(0) uncertainty (real space) i0_real_error1.8320e+07
Rg (reciprocal space) rg_reciprocal15.48 Å
I(0) (reciprocal space) i0_reciprocal1691000000.0000
Solution quality estimate total_estimate0.7903
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.3 Å
Skewness Skewness skewness0.285
Kurtosis Kurtosis kurtosis-0.159
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha616800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1de3a_
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 (1 domains)

Domain ID domain_id1de3A00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
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8. Citations (3)

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9. Files and Curves (10)