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- PDB-4g9j: Protein Ser/Thr phosphatase-1 in complex with cell-permeable peptide -

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Basic information

Entry
Database: PDB / ID: 4g9j
TitleProtein Ser/Thr phosphatase-1 in complex with cell-permeable peptide
Components
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
  • synthetic peptide
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / protein phosphatase 1 / activating peptide / RVxF binding motif / HYDROLASE-HYDROLASE ACTIVATOR complex
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 / branching morphogenesis of an epithelial tube ...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 / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / dephosphorylation / myosin phosphatase activity / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / Maturation of hRSV A proteins / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / DARPP-32 events / transition metal ion binding / ribonucleoprotein complex binding / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / lung development / response to lead ion / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / iron ion binding / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...: / 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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsSukackaite, R. / Chatterjee, J. / Beullens, M. / Bollen, M. / Koehn, M. / Hart, D.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Development of a Peptide that Selectively Activates Protein Phosphatase-1 in Living Cells.
Authors: Chatterjee, J. / Beullens, M. / Sukackaite, R. / Qian, J. / Lesage, B. / Hart, D.J. / Bollen, M. / Kohn, M.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: synthetic peptide
D: synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9516
Polymers80,8414
Non-polymers1102
Water61334
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4753
Polymers40,4202
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-16 kcal/mol
Surface area13080 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4753
Polymers40,4202
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-18 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.007, 138.007, 113.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 37615.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1A, PPP1CA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein/peptide synthetic peptide


Mass: 2805.377 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: sitting drop / pH: 8
Details: 20% PEG6000, 1 M lithium chloride, pH 8.0, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1271 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2011
RadiationMonochromator: channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3→97.586 Å / Num. all: 22560 / Num. obs: 22186 / % possible obs: 99 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.16-3.335.90.6641.21625027650.66499.7
3.33-3.536.10.372.11599726100.3799.6
3.53-3.785.90.2632.91449024410.26399
3.78-4.086.10.1594.81396622910.15999.2
4.08-4.4760.0987.71271621280.09899.2
4.47-560.0838.81132319030.08398.4
5-5.776.10.0977.71039517120.09798.7
5.77-7.075.80.0848.7842414460.08498.6
7.07-9.995.70.05212.3661911540.05298
9.99-49.115.20.0413.235046690.0496.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALA3.2.19data scaling
PDB_EXTRACT3.006data extraction
MxCuBEdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FJM

1fjm


Resolution: 3.1→97.586 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.864 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.793 / SU B: 21.046 / SU ML: 0.369 / SU Rfree: 0.443 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 928 4.6 %RANDOM
Rwork0.224 ---
obs0.226 20157 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.57 Å2 / Biso mean: 60.665 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---0.97 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 3.1→97.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4908 0 2 34 4944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225016
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9696776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4075608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28624.104251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23115871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.841534
X-RAY DIFFRACTIONr_chiral_restr0.0390.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023844
X-RAY DIFFRACTIONr_nbd_refined0.190.22276
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.22
X-RAY DIFFRACTIONr_mcbond_it0.7631.53125
X-RAY DIFFRACTIONr_mcangle_it1.3724884
X-RAY DIFFRACTIONr_scbond_it1.61932132
X-RAY DIFFRACTIONr_scangle_it2.7314.51892
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 62 -
Rwork0.312 1429 -
all-1491 -
obs--99.47 %

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