5wwm

Crystal structure of the TPR domain of Rrp5

Method: X-RAY DIFFRACTION Dmax: 85.6 Å Quality: GOOD

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

rRNA biogenesis protein RRP5

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q05022

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 1399–1729 Fragment:UNP residues 1399-1729 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;0.5M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium citrate, pH 5.6 Resolution 2.81 Å R-free 0.258

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 RRP5_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–331; UniProt 1399–1729

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 5wwm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5wwm
Deposition date deposition_date2017-01-03
Structure title titleCrystal structure of the TPR domain of Rrp5
Keywords keywordsRNA binding protein, component of 90S preribosome; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.63
Radius of gyration Rg (electron density) rg_electron25.24
Forward intensity I(0) i016618500.00
Molecular weight molecular_weight31804.0 kDa
Excluded volume excluded_volume40079 ų
Envelope volume envelope_volume53297 ų
Hydration-shell volume shell_volume18432 ų
Envelope diameter envelope_diameter84.9
Shell Rg shell_rg31.36
Envelope Rg envelope_rg25.27
Shape Rg shape_rg25.22
Total Rg total_rg26.06
Total atoms total_atoms2243
Residues n_residues272
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 dmax85.6
Rg (real space) rg_real25.80
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real1.6620e+07
I(0) uncertainty (real space) i0_real_error2.4120e+05
Rg (reciprocal space) rg_reciprocal25.75
I(0) (reciprocal space) i0_reciprocal16620000.0000
Solution quality estimate total_estimate0.8436
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary20.7
Skewness Skewness skewness0.403
Kurtosis Kurtosis kurtosis-0.645
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4975000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.694; Smooth: 0.980

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)