5r0f

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry D06, DMSO-free

Method: X-RAY DIFFRACTION Dmax: 110.8 Å Quality: GOOD

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

Pre-mRNA-splicing factor 8

Saccharomyces cerevisiae (strain ATCC 204508 / 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:yPrp8 RNaseH (UNP Residues 1836-2096) A1 cistron-splicing factor AAR2 × 1 (P32357) R9G (3-methoxyphenyl)(pyrrolidin-1-yl)methanone × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 4000, 0.2M Tris-HCl pH 8.5, 0.2M Li2SO4 Resolution 1.97 Å R-free 0.304

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 (strain ATCC 204508 / 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 Fragment:GAMA - Aar2(1-152) - SSSSS - Aar2(171-317) Mutation:L153_D170delinsSSSSS Pre-mRNA-splicing factor 8 × 1 (P33334) R9G (3-methoxyphenyl)(pyrrolidin-1-yl)methanone × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 4000, 0.2M Tris-HCl pH 8.5, 0.2M Li2SO4 Resolution 1.97 Å R-free 0.304

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 5r0f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5r0f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5r0f
Deposition date deposition_date2020-02-12
Structure title titlePanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry D06, DMSO-free
Keywords keywordsFragMAX, FragMAXapp, fragment screening, RNaseH like domain, VHS 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_guinier32.61
Radius of gyration Rg (electron density) rg_electron32.43
Forward intensity I(0) i059862200.00
Molecular weight molecular_weight62704.0 kDa
Excluded volume excluded_volume78896 ų
Envelope volume envelope_volume102200 ų
Hydration-shell volume shell_volume27778 ų
Envelope diameter envelope_diameter118.7
Shell Rg shell_rg37.20
Envelope Rg envelope_rg32.28
Shape Rg shape_rg32.43
Total Rg total_rg32.83
Total atoms total_atoms4417
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 dmax110.8
Rg (real space) rg_real33.01
Rg uncertainty (real space) rg_real_error1.34
I(0) (real space) i0_real5.9860e+07
I(0) uncertainty (real space) i0_real_error1.0080e+06
Rg (reciprocal space) rg_reciprocal32.84
I(0) (reciprocal space) i0_reciprocal59850000.0000
Solution quality estimate total_estimate0.8190
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.1
Skewness Skewness skewness0.508
Kurtosis Kurtosis kurtosis-0.465
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11670000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.704; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.668; Smooth: 0.870

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5r0fa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.14 — Prp8 beta-finger domain-like
Domain ID domain_idd5r0fa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5r0fb1
Class classb — All beta proteins
Fold Fold foldb.182 — U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like
Superfamily Superfamily superfamilyb.182.1 — U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like
Family Family familyb.182.1.1 — U5 small nuclear riboprotein particle assembly factor Aar2 N-terminal domain-like
Domain ID domain_idd5r0fb2
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.29 — U5 small nuclear riboprotein particle assembly factor Aar2 C-terminal domain-like
Family Family familya.118.29.1 — U5 small nuclear riboprotein particle assembly factor Aar2 C-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id5r0fB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily20
Domain ID domain_id5r0fB02
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)