6obu

PP1 Y134K in complex with Microcystin LR

Method: X-RAY DIFFRACTION Dmax: 87.4 Å Quality: REASONABLE

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 Fragment:UNP residues 7-300 Mutation:Y134K Microcystin LR × 1 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 5 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;289 K;20% PEG6000, 1 M lithium chloride, 0.1 M MES, pH 6.0 Resolution 1.95 Å R-free 0.202
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 7–300 Fragment:UNP residues 7-300 Mutation:Y134K Microcystin LR × 1 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;289 K;20% PEG6000, 1 M lithium chloride, 0.1 M MES, pH 6.0 Resolution 1.95 Å R-free 0.202

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 B; PDBConstruct 6–299; UniProt 7–300

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 6obu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6obu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6obu
Deposition date deposition_date2019-03-21
Structure title titlePP1 Y134K in complex with Microcystin LR
Keywords keywordsphosphatase, HYDROLASE-TOXIN complex; HYDROLASE/TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.50
Radius of gyration Rg (electron density) rg_electron26.73
Forward intensity I(0) i074716500.00
Molecular weight molecular_weight68853.0 kDa
Excluded volume excluded_volume86559 ų
Envelope volume envelope_volume99945 ų
Hydration-shell volume shell_volume31221 ų
Envelope diameter envelope_diameter92.2
Shell Rg shell_rg33.93
Envelope Rg envelope_rg26.78
Shape Rg shape_rg26.71
Total Rg total_rg27.55
Total atoms total_atoms4825
Residues n_residues590
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 dmax87.4
Rg (real space) rg_real27.51
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real7.4720e+07
I(0) uncertainty (real space) i0_real_error1.0450e+06
Rg (reciprocal space) rg_reciprocal27.51
I(0) (reciprocal space) i0_reciprocal74720000.0000
Solution quality estimate total_estimate0.7280
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.338
Kurtosis Kurtosis kurtosis-0.544
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32760000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 0.267; Positv: 1.000; Valcen: 0.990; Smooth: 0.965

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6obua_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd6obub_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase

CATH v4.4 (2 domains)

Domain ID domain_id6obuA00
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_id6obuB00
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)