5m9m

Human angiogenin PD variant Q77P

Method: X-RAY DIFFRACTION Dmax: 84.1 Å Quality: EXCELLENT

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 25–147 Not recorded SO4 SULFATE ION × 2 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;289 K;0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350 Resolution 1.65 Å R-free 0.270
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 25–147 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;289 K;0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350 Resolution 1.65 Å R-free 0.270
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 25–147 Not recorded SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;289 K;0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350 Resolution 1.65 Å R-free 0.270
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 25–147 Not recorded SO4 SULFATE ION × 4 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;289 K;0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350 Resolution 1.65 Å R-free 0.270

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 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ANGI_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–124; UniProt 25–147 Author chain B; PDBConstruct 2–124; UniProt 25–147 Author chain C; PDBConstruct 2–124; UniProt 25–147 Author chain D; PDBConstruct 2–124; 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 5m9m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5m9m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5m9m
Deposition date deposition_date2016-11-01
Structure title titleHuman angiogenin PD variant Q77P
Keywords keywords;Parkinson's, RNase, angiogenesis, hydrolase ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.42
Radius of gyration Rg (electron density) rg_electron25.60
Forward intensity I(0) i062475400.00
Molecular weight molecular_weight56219.0 kDa
Excluded volume excluded_volume68280 ų
Envelope volume envelope_volume88082 ų
Hydration-shell volume shell_volume28842 ų
Envelope diameter envelope_diameter89.9
Shell Rg shell_rg32.55
Envelope Rg envelope_rg25.58
Shape Rg shape_rg25.60
Total Rg total_rg26.34
Total atoms total_atoms3921
Residues n_residues476
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 dmax84.1
Rg (real space) rg_real26.29
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real6.2480e+07
I(0) uncertainty (real space) i0_real_error8.7770e+05
Rg (reciprocal space) rg_reciprocal26.33
I(0) (reciprocal space) i0_reciprocal62480000.0000
Solution quality estimate total_estimate0.9019
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary82.7
Skewness Skewness skewness0.145
Kurtosis Kurtosis kurtosis-0.465
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10130000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5m9ma_
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
Domain ID domain_idd5m9mb_
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
Domain ID domain_idd5m9mc_
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
Domain ID domain_idd5m9md_
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 (4 domains)

Domain ID domain_id5m9mA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology130 — P-30 Protein
Homologous superfamily homologous superfamily10 — Ribonuclease A-like domain
Domain ID domain_id5m9mB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology130 — P-30 Protein
Homologous superfamily homologous superfamily10 — Ribonuclease A-like domain
Domain ID domain_id5m9mC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology130 — P-30 Protein
Homologous superfamily homologous superfamily10 — Ribonuclease A-like domain
Domain ID domain_id5m9mD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology130 — P-30 Protein
Homologous superfamily homologous superfamily10 — Ribonuclease A-like domain

8. Citations (1)

9. Files and Curves (10)