8vmo

Homing endonuclease I-PpoI-DNA complex:ground state at pH7.0 (K+ MES) with Na+

Method: X-RAY DIFFRACTION Dmax: 80.4 Å Quality: REASONABLE

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

Intron-encoded endonuclease I-PpoI

Physarum polycephalum

UniProt Q94702

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 2–163 Chain B; UniProt 2–163 Not recorded ;DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3') ; × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;0.2 M Sodium Malonate, PEG 3350, 0.1 M MES Resolution 1.68 Å R-free 0.189

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.

49 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PPO1_PHYPO
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–162; UniProt 2–163 Author chain B; PDBConstruct 1–162; UniProt 2–163

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 8vmo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8vmo
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id8vmo
Deposition date deposition_date2024-01-13
Structure title titleHoming endonuclease I-PpoI-DNA complex:ground state at pH7.0 (K+ MES) with Na+
Keywords keywordsIntron encoded homing endonuclease I-PpoI, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.81
Radius of gyration Rg (electron density) rg_electron24.53
Forward intensity I(0) i056019200.00
Molecular weight molecular_weight48967.0 kDa
Excluded volume excluded_volume57081 ų
Envelope volume envelope_volume71737 ų
Hydration-shell volume shell_volume24905 ų
Envelope diameter envelope_diameter81.0
Shell Rg shell_rg31.43
Envelope Rg envelope_rg24.62
Shape Rg shape_rg24.54
Total Rg total_rg25.14
Total atoms total_atoms3380
Residues n_residues366
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 dmax80.4
Rg (real space) rg_real24.85
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real5.6020e+07
I(0) uncertainty (real space) i0_real_error6.8710e+05
Rg (reciprocal space) rg_reciprocal24.84
I(0) (reciprocal space) i0_reciprocal56020000.0000
Solution quality estimate total_estimate0.6726
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.8
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5925000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 0.036; Positv: 1.000; Valcen: 0.948; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (2)

9. Files and Curves (10)