7fm3

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment P05H09 from the F2X-Universal Library

Method: X-RAY DIFFRACTION Dmax: 111.9 Å Quality: GOOD

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

Pre-mRNA-splicing factor 8

Saccharomyces cerevisiae S288C

UniProt P33334

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1836–2090 Fragment:UNP residues 1836-2090 A1 cistron-splicing factor AAR2 × 1 (P32357) VSL methyl 4,5,6,7-tetrahydro-2H-indazole-3-carboxylate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;19% PEG4000, 3% DMSO, 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate Resolution 1.65 Å R-free 0.317

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.

435 other PDB entries and 443 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRP8_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–258; UniProt 1836–2090

A1 cistron-splicing factor AAR2

Saccharomyces cerevisiae S288C

UniProt P32357

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–317 Not recorded Pre-mRNA-splicing factor 8 × 1 (P33334) VSL methyl 4,5,6,7-tetrahydro-2H-indazole-3-carboxylate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;19% PEG4000, 3% DMSO, 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate Resolution 1.65 Å R-free 0.317

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.

400 other PDB entries and 403 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AAR2_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 5–308; UniProt 1–317

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 7fm3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7fm3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7fm3
Deposition date deposition_date2022-08-26
Structure title titlePanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment P05H09 from the F2X-Universal Library
Keywords keywordsFRAGMAX, FRAGMAXAPP, fragment screening, RNaseH like domain, U5 SNRNP assembly, SPLICING; SPLICING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.93
Radius of gyration Rg (electron density) rg_electron32.80
Forward intensity I(0) i059962700.00
Molecular weight molecular_weight62767.0 kDa
Excluded volume excluded_volume78962 ų
Envelope volume envelope_volume102770 ų
Hydration-shell volume shell_volume27706 ų
Envelope diameter envelope_diameter120.3
Shell Rg shell_rg37.37
Envelope Rg envelope_rg32.61
Shape Rg shape_rg32.80
Total Rg total_rg33.18
Total atoms total_atoms8741
Residues n_residues537
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 dmax111.9
Rg (real space) rg_real33.36
Rg uncertainty (real space) rg_real_error1.06
I(0) (real space) i0_real5.9960e+07
I(0) uncertainty (real space) i0_real_error9.7990e+05
Rg (reciprocal space) rg_reciprocal33.18
I(0) (reciprocal space) i0_reciprocal59950000.0000
Solution quality estimate total_estimate0.8104
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.0
Skewness Skewness skewness0.514
Kurtosis Kurtosis kurtosis-0.467
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11240000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.711; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.603; Smooth: 0.794

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7fm3B01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily550 — Aar2, C-terminal domain-like

8. Citations (1)

9. Files and Curves (10)