7t0y

The Ribosomal RNA Processing 1B Protein Phosphatase-1 Holoenzyme

Method: X-RAY DIFFRACTION Dmax: 90.0 Å Quality: GOOD

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

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

Homo sapiens

UniProt P62136

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 7–300 Mutation:Q20R Ribosomal RNA processing protein 1 homolog B × 1 (Q14684) EDO 1,2-ETHANEDIOL × 5 MN MANGANESE (II) ION × 2 F FLUORIDE ION × 1 BR BROMIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;20% ethylene glycol; 10% PEG8000, 0.1 M imidazole; MES acid, 0.09 M Sodium fluoride; 0.09 M Sodium bromide; 0.09 M Sodium iodide Resolution 1.80 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 7–300 Mutation:Q20R Ribosomal RNA processing protein 1 homolog B × 1 (Q14684) EDO 1,2-ETHANEDIOL × 6 MN MANGANESE (II) ION × 2 BR BROMIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;20% ethylene glycol; 10% PEG8000, 0.1 M imidazole; MES acid, 0.09 M Sodium fluoride; 0.09 M Sodium bromide; 0.09 M Sodium iodide Resolution 1.80 Å R-free 0.246

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.

45 other PDB entries and 87 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PP1A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–299; UniProt 7–300 Author chain C; PDBConstruct 6–299; UniProt 7–300

Ribosomal RNA processing protein 1 homolog B

Homo sapiens

UniProt Q14684

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 682–727 Not recorded Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) EDO 1,2-ETHANEDIOL × 5 MN MANGANESE (II) ION × 2 F FLUORIDE ION × 1 BR BROMIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;20% ethylene glycol; 10% PEG8000, 0.1 M imidazole; MES acid, 0.09 M Sodium fluoride; 0.09 M Sodium bromide; 0.09 M Sodium iodide Resolution 1.80 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 682–727 Not recorded Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) EDO 1,2-ETHANEDIOL × 6 MN MANGANESE (II) ION × 2 BR BROMIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;289 K;20% ethylene glycol; 10% PEG8000, 0.1 M imidazole; MES acid, 0.09 M Sodium fluoride; 0.09 M Sodium bromide; 0.09 M Sodium iodide Resolution 1.80 Å R-free 0.246

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RRP1B_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–47; UniProt 682–727 Author chain D; PDBConstruct 2–47; UniProt 682–727

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 7t0y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7t0y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7t0y
Deposition date deposition_date2021-11-30
Structure title titleThe Ribosomal RNA Processing 1B Protein Phosphatase-1 Holoenzyme
Keywords keywordsProtein Binding, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.58
Radius of gyration Rg (electron density) rg_electron27.97
Forward intensity I(0) i0100945000.00
Molecular weight molecular_weight79474.0 kDa
Excluded volume excluded_volume99470 ų
Envelope volume envelope_volume118980 ų
Hydration-shell volume shell_volume35117 ų
Envelope diameter envelope_diameter95.2
Shell Rg shell_rg35.69
Envelope Rg envelope_rg27.92
Shape Rg shape_rg27.94
Total Rg total_rg28.81
Total atoms total_atoms5556
Residues n_residues690
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 dmax90.0
Rg (real space) rg_real28.56
Rg uncertainty (real space) rg_real_error0.65
I(0) (real space) i0_real1.0090e+08
I(0) uncertainty (real space) i0_real_error1.5580e+06
Rg (reciprocal space) rg_reciprocal28.57
I(0) (reciprocal space) i0_reciprocal100900000.0000
Solution quality estimate total_estimate0.8997
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.318
Kurtosis Kurtosis kurtosis-0.504
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33170000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.941

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7t0yA01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id7t0yC01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases

8. Citations (1)

9. Files and Curves (10)