9owy

Structure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with loop-back 5' leader (sub-conformation 2 of tRNA anticodon arm tilted)

Method: ELECTRON MICROSCOPY Dmax: 153.5 Å Quality: GOOD

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

Ribonuclease P protein component

Geobacillus stearothermophilus

UniProt A0A150N245

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 Monomer Protein × 1 RNA 2 PDB declaration: trimeric(3) Consistent with all polymer counts Chain B; UniProt 1–115 Not recorded RNase P RNA (417-MER) × 1 precursor tRNA (108-MER) × 1 CALCIUM ION × 29 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 2.69 Å

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.

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A150N245_GEOSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–116; UniProt 1–115

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 9owy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9owy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9owy
Deposition date deposition_date2025-06-02
Structure title titleStructure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with loop-back 5' leader (sub-conformation 2 of tRNA anticodon arm tilted)
Keywords keywordsribozyme, RNA, RNase P., RNA-Hydrolase complex; RNA/Hydrolase
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier44.62
Radius of gyration Rg (electron density) rg_electron44.47
Forward intensity I(0) i01434760000.00
Molecular weight molecular_weight185200.0 kDa
Excluded volume excluded_volume177470 ų
Envelope volume envelope_volume300440 ų
Hydration-shell volume shell_volume59399 ų
Envelope diameter envelope_diameter161.4
Shell Rg shell_rg46.36
Envelope Rg envelope_rg43.56
Shape Rg shape_rg44.46
Total Rg total_rg44.53
Total atoms total_atoms12231
Residues n_residues641
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 dmax153.5
Rg (real space) rg_real44.71
Rg uncertainty (real space) rg_real_error1.46
I(0) (real space) i0_real1.4350e+09
I(0) uncertainty (real space) i0_real_error2.5960e+07
Rg (reciprocal space) rg_reciprocal44.62
I(0) (reciprocal space) i0_reciprocal1435000000.0000
Solution quality estimate total_estimate0.8701
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.3
Skewness Skewness skewness0.392
Kurtosis Kurtosis kurtosis-0.223
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41900000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.794

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)