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- PDB-6obs: PP1 Y134K -

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Basic information

Entry
Database: PDB / ID: 6obs
TitlePP1 Y134K
ComponentsSerine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / phosphatase
Function / homology
Function and homology information


regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress ...regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / glycogen metabolic process / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / lung development / Downregulation of TGF-beta receptor signaling / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / response to lead ion / : / presynapse / perikaryon / dendritic spine / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / 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 / 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
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsChoy, M.S. / Moon, T.M. / Bray, J.A. / Archuleta, T.L. / Shi, W. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: SDS22 selectively recognizes and traps metal-deficient inactive PP1.
Authors: Choy, M.S. / Moon, T.M. / Ravindran, R. / Bray, J.A. / Robinson, L.C. / Archuleta, T.L. / Shi, W. / Peti, W. / Tatchell, K. / Page, R.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7589
Polymers68,2562
Non-polymers5027
Water9,098505
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4255
Polymers34,1281
Non-polymers2974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3334
Polymers34,1281
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.094, 76.794, 131.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34128.156 Da / Num. of mol.: 2 / Fragment: UNP residues 7-300 / Mutation: Y134K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG6000, 1 M lithium chloride, 0.1 M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.8→17.73 Å / Num. obs: 61204 / % possible obs: 99.6 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.489 / Num. unique obs: 9365 / CC1/2: 0.571

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MOV

4mov


Resolution: 1.803→17.73 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2461 3168 5.17 %
Rwork0.2042 --
obs0.2064 61204 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.803→17.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 20 505 5173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014815
X-RAY DIFFRACTIONf_angle_d0.8186490
X-RAY DIFFRACTIONf_dihedral_angle_d15.4452868
X-RAY DIFFRACTIONf_chiral_restr0.05703
X-RAY DIFFRACTIONf_plane_restr0.004846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8033-1.82380.37621840.35943381X-RAY DIFFRACTION91
1.8238-1.84530.37521780.32473672X-RAY DIFFRACTION100
1.8453-1.86770.3411820.31883768X-RAY DIFFRACTION100
1.8677-1.89130.33621850.30833695X-RAY DIFFRACTION100
1.8913-1.91620.32742080.28073715X-RAY DIFFRACTION100
1.9162-1.94240.3022350.25833654X-RAY DIFFRACTION100
1.9424-1.97010.26792160.24543752X-RAY DIFFRACTION100
1.9701-1.99950.28891750.23423679X-RAY DIFFRACTION100
1.9995-2.03070.29891880.2333745X-RAY DIFFRACTION100
2.0307-2.0640.26072250.22773688X-RAY DIFFRACTION100
2.064-2.09950.24862100.21733723X-RAY DIFFRACTION100
2.0995-2.13760.25431700.22143706X-RAY DIFFRACTION100
2.1376-2.17860.27762300.2213698X-RAY DIFFRACTION100
2.1786-2.2230.25822020.20563679X-RAY DIFFRACTION100
2.223-2.27130.2722170.2063691X-RAY DIFFRACTION100
2.2713-2.3240.21731980.19263723X-RAY DIFFRACTION100
2.324-2.3820.24912120.19663697X-RAY DIFFRACTION100
2.382-2.44620.25642160.18583686X-RAY DIFFRACTION100
2.4462-2.5180.24911830.18993720X-RAY DIFFRACTION100
2.518-2.59910.22262020.19393727X-RAY DIFFRACTION100
2.5991-2.69160.27312230.19243642X-RAY DIFFRACTION100
2.6916-2.7990.25562080.18873736X-RAY DIFFRACTION100
2.799-2.92590.25252190.18723664X-RAY DIFFRACTION100
2.9259-3.07940.20471910.18623757X-RAY DIFFRACTION100
3.0794-3.27120.23961520.18053742X-RAY DIFFRACTION100
3.2712-3.52190.20272040.17983694X-RAY DIFFRACTION100
3.5219-3.8730.24852100.17483712X-RAY DIFFRACTION100
3.873-4.42580.18612090.17563673X-RAY DIFFRACTION100
4.4258-5.54760.21742110.17243694X-RAY DIFFRACTION100
5.5476-17.73350.21332030.20983706X-RAY DIFFRACTION100

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