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- PDB-8sw5: Protein Phosphatase 1 in complex with PP1-specific Phosphatase ta... -

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Basic information

Entry
Database: PDB / ID: 8sw5
TitleProtein Phosphatase 1 in complex with PP1-specific Phosphatase targeting peptide (PhosTAP) version 1
Components
  • PP1-specific Phosphatase-Targeting Peptide version 1
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsBIOSYNTHETIC PROTEIN / Phosphatase-targeting peptide / complex / phosphatase regulator
Function / homology
Function and homology information


regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity ...regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / cell cycle / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsChoy, M.S. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: A Protein Phosphatase 1 specific phosphatase targeting peptide (PhosTAP) to identify the PP1 phosphatome
Authors: Choy, M.S. / Nguyen, H.T. / Kettenbach, A.N. / Peti, W. / Page, R.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: PP1-specific Phosphatase-Targeting Peptide version 1
D: PP1-specific Phosphatase-Targeting Peptide version 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,23110
Polymers79,8214
Non-polymers4106
Water1,49583
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: PP1-specific Phosphatase-Targeting Peptide version 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1165
Polymers39,9112
Non-polymers2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-38 kcal/mol
Surface area13460 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: PP1-specific Phosphatase-Targeting Peptide version 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1165
Polymers39,9112
Non-polymers2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-38 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.876, 92.876, 200.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein/peptide PP1-specific Phosphatase-Targeting Peptide version 1


Mass: 5748.560 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.6
Details: 1 M ammonium dihydrogen phosphate, 100 mM tri-sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.39→38.36 Å / Num. obs: 35238 / % possible obs: 98.4 % / Redundancy: 16.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.025 / Rrim(I) all: 0.103 / Net I/σ(I): 17.6 / Num. measured all: 593152
Reflection shellResolution: 2.39→2.48 Å / % possible obs: 85.3 % / Redundancy: 11.1 % / Rmerge(I) obs: 1.869 / Num. measured all: 34537 / Num. unique obs: 3111 / CC1/2: 0.569 / Rpim(I) all: 0.57 / Rrim(I) all: 1.96 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→38.36 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 1999 5.73 %
Rwork0.2098 --
obs0.2121 34883 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 14 83 5185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025257
X-RAY DIFFRACTIONf_angle_d0.6757117
X-RAY DIFFRACTIONf_dihedral_angle_d13.0991948
X-RAY DIFFRACTIONf_chiral_restr0.043766
X-RAY DIFFRACTIONf_plane_restr0.004921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.32931150.33471901X-RAY DIFFRACTION81
2.45-2.520.34131420.29692332X-RAY DIFFRACTION100
2.52-2.590.2661430.26612329X-RAY DIFFRACTION100
2.59-2.680.3321410.27342345X-RAY DIFFRACTION100
2.68-2.770.31081430.26212340X-RAY DIFFRACTION100
2.77-2.880.27121440.27412363X-RAY DIFFRACTION100
2.88-3.010.29541420.26622345X-RAY DIFFRACTION100
3.01-3.170.31081440.25482358X-RAY DIFFRACTION100
3.17-3.370.27461450.24822378X-RAY DIFFRACTION100
3.37-3.630.27231440.21922379X-RAY DIFFRACTION100
3.63-40.29491420.21582340X-RAY DIFFRACTION98
4-4.570.19551460.16072409X-RAY DIFFRACTION100
4.57-5.760.20831500.17522464X-RAY DIFFRACTION100
5.76-38.360.22781580.18042601X-RAY DIFFRACTION100

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