1yvs

Trimeric domain swapped barnase

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: REASONABLE

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

BARNASE

Bacillus amyloliquefaciens

UniProt P00648

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 48–157 Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.5;pH 4.5 Resolution 2.20 Å R-free 0.244
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 48–157 Not recorded SO4 SULFATE ION × 12 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.5;pH 4.5 Resolution 2.20 Å R-free 0.244

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.

51 other PDB entries and 136 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNBR_BACAM
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–110; UniProt 48–157

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 1yvs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1yvs
Deposition date deposition_date1998-12-10
Structure title titleTrimeric domain swapped barnase
Keywords keywordsENDONUCLEASE, RIBONUCLEASE, DOMAIN SWAPPED, TRIMER; ENDONUCLEASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.19
Radius of gyration Rg (electron density) rg_electron22.71
Forward intensity I(0) i03170650.00
Molecular weight molecular_weight12378.0 kDa
Excluded volume excluded_volume15321 ų
Envelope volume envelope_volume22604 ų
Hydration-shell volume shell_volume10154 ų
Envelope diameter envelope_diameter77.3
Shell Rg shell_rg25.00
Envelope Rg envelope_rg22.63
Shape Rg shape_rg22.73
Total Rg total_rg23.05
Total atoms total_atoms874
Residues n_residues108
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 dmax78.8
Rg (real space) rg_real22.72
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real3.1710e+06
I(0) uncertainty (real space) i0_real_error4.5520e+04
Rg (reciprocal space) rg_reciprocal22.63
I(0) (reciprocal space) i0_reciprocal3170000.0000
Solution quality estimate total_estimate0.7207
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary16.5
Skewness Skewness skewness0.587
Kurtosis Kurtosis kurtosis-0.521
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha280800.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.433; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.088; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1yvsa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.2 — Bacterial ribonucleases

CATH v4.4 (1 domains)

Domain ID domain_id1yvsA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases

8. Citations (1)

9. Files and Curves (10)