4xpn

Crystal Structure of Protein Phosphate 1 complexed with PP1 binding domain of GADD34

Method: X-RAY DIFFRACTION Dmax: 93.0 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 Fragment:UNP residues 7-300 Protein phosphatase 1 regulatory subunit 15A × 1 (O75807) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.8;277 K;0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350 Resolution 2.29 Å R-free 0.205
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 7–300 Fragment:UNP residues 7-300 Protein phosphatase 1 regulatory subunit 15A × 1 (O75807) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.8;277 K;0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350 Resolution 2.29 Å R-free 0.205

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

Protein phosphatase 1 regulatory subunit 15A

Homo sapiens

UniProt O75807

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 552–591 Fragment:UNP residues 552-591 Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.8;277 K;0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350 Resolution 2.29 Å R-free 0.205
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 552–591 Fragment:UNP residues 552-591 Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.8;277 K;0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350 Resolution 2.29 Å R-free 0.205

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.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PR15A_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–43; UniProt 552–591 Author chain D; PDBConstruct 4–43; UniProt 552–591

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 4xpn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4xpn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4xpn
Deposition date deposition_date2015-01-17
Structure title titleCrystal Structure of Protein Phosphate 1 complexed with PP1 binding domain of GADD34
Keywords keywordseIF2alpha phosphatase, PP1 regulator, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.42
Radius of gyration Rg (electron density) rg_electron28.09
Forward intensity I(0) i078563600.00
Molecular weight molecular_weight70476.0 kDa
Excluded volume excluded_volume88352 ų
Envelope volume envelope_volume103500 ų
Hydration-shell volume shell_volume31150 ų
Envelope diameter envelope_diameter95.1
Shell Rg shell_rg34.89
Envelope Rg envelope_rg28.20
Shape Rg shape_rg28.09
Total Rg total_rg28.75
Total atoms total_atoms4943
Residues n_residues620
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 dmax93.0
Rg (real space) rg_real28.55
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real7.8560e+07
I(0) uncertainty (real space) i0_real_error1.1200e+06
Rg (reciprocal space) rg_reciprocal28.51
I(0) (reciprocal space) i0_reciprocal78560000.0000
Solution quality estimate total_estimate0.8682
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary91.4
Skewness Skewness skewness0.426
Kurtosis Kurtosis kurtosis-0.476
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40370000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.882

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4xpna1
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_idd4xpna2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4xpnc1
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_idd4xpnc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id4xpnA00
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_id4xpnC00
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)