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1bc4

THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTES OF RANA CATESBEIANA (BULLFROG), NMR, 15 STRUCTURES

Method: SOLUTION NMR Dmax: 47.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBONUCLEASE

OrganismNot specified

UniProt P11916

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 2–111 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 3.5；305 K；Ionic strength (raw mmCIF value) 50mM PHOSPHATE BUFFER；Pressure 1 NMR sample composition：H2O 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 1BC4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1KM8 The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog) Deposited 2001-12-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–111（111 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ammonium phosphate, Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.205
1KM9 The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog) Deposited 2001-12-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–111（111 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4000, ammonium phosphate, NaOAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.96 Å R-free 0.216
1M07 RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA) Deposited 2002-06-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–111（111 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1 M potassium sodium tartrate tetrahydrate, 24 % PEG 8000, 0.05 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.228
1M07 RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA) Deposited 2002-06-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 1–111（111 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1 M potassium sodium tartrate tetrahydrate, 24 % PEG 8000, 0.05 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.228

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

View Construct and Data Evidence
UniProt name RNASO_RANCA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–111； UniProt 2–111

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 1bc4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bc4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bc4
Deposition date deposition_date1998-05-05
Structure title titleTHE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTES OF RANA CATESBEIANA (BULLFROG), NMR, 15 STRUCTURES
Keywords keywordsHYDROLASE, PHOSPHORIC DIESTER, RC-RNASE, CYTOTOXIC PROTEIN, SIALIC ACID BINDING LECTIN; 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_guinier14.62 Å
Radius of gyration Rg (electron density) rg_electron14.50 Å
Forward intensity I(0) i0517917000.00
Molecular weight molecular_weight186820.0 kDa
Excluded volume excluded_volume231850 ų
Envelope volume envelope_volume27399 ų
Hydration-shell volume shell_volume14634 ų
Envelope diameter envelope_diameter54.8 Å
Shell Rg shell_rg21.71 Å
Envelope Rg envelope_rg16.24 Å
Shape Rg shape_rg14.46 Å
Total Rg total_rg14.82 Å
Total atoms total_atoms25935
Residues n_residues1650
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 dmax47.4 Å
Rg (real space) rg_real14.60 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real5.1790e+08
I(0) uncertainty (real space) i0_real_error5.3650e+06
Rg (reciprocal space) rg_reciprocal14.60 Å
I(0) (reciprocal space) i0_reciprocal517900000.0000
Solution quality estimate total_estimate0.8250
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary15.6 Å
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.458
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha304300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; 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_idd1bc4a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.5 — RNase A-like
Superfamily Superfamily superfamilyd.5.1 — RNase A-like
Family Family familyd.5.1.1 — Ribonuclease A-like

CATH v4.4 (1 domains)

Domain ID domain_id1bc4A00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology130 — P-30 Protein
Homologous superfamily homologous superfamily10 — Ribonuclease A-like domain
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8. Citations (2)

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9. Files and Curves (10)