8af0

Crystal structure of human angiogenin and RNA duplex

Method: X-RAY DIFFRACTION Dmax: 74.2 Å Quality: REASONABLE

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

Angiogenin

Homo sapiens

UniProt P03950

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–RNA Homooligomer Protein × 2 RNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 25–147 Chain B; UniProt 25–147 Mutation:H114A ;RNA (5'-R(*GP*CP*CP*CP*GP*CP*CP*UP*GP*UP*CP*AP*CP*GP*CP*GP*GP*GP*C)-3') ; × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;200 mM NaCl, 20 % (w/v) PEG6000, 100 mM Hepes pH 7.0 Resolution 2.43 Å R-free 0.268

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.

53 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ANGI_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–123; UniProt 25–147 Author chain B; PDBConstruct 1–123; UniProt 25–147

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 8af0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8af0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8af0
Deposition date deposition_date2022-07-15
Structure title titleCrystal structure of human angiogenin and RNA duplex
Keywords keywordsribonuclease, RNA duplex, RNase A-like, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.15
Radius of gyration Rg (electron density) rg_electron23.67
Forward intensity I(0) i043523800.00
Molecular weight molecular_weight40526.0 kDa
Excluded volume excluded_volume46186 ų
Envelope volume envelope_volume62864 ų
Hydration-shell volume shell_volume22589 ų
Envelope diameter envelope_diameter76.1
Shell Rg shell_rg30.02
Envelope Rg envelope_rg23.39
Shape Rg shape_rg23.65
Total Rg total_rg24.33
Total atoms total_atoms2791
Residues n_residues284
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 dmax74.2
Rg (real space) rg_real24.05
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real4.3520e+07
I(0) uncertainty (real space) i0_real_error5.5050e+05
Rg (reciprocal space) rg_reciprocal24.08
I(0) (reciprocal space) i0_reciprocal43520000.0000
Solution quality estimate total_estimate0.7065
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.5
Skewness Skewness skewness0.157
Kurtosis Kurtosis kurtosis-0.527
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2993000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)