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- PDB-6alz: Crystal structure of Protein Phosphatase 1 bound to the natural i... -

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Basic information

Entry
Database: PDB / ID: 6alz
TitleCrystal structure of Protein Phosphatase 1 bound to the natural inhibitor Tautomycetin
ComponentsSerine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / RNA polymerase II promoter clearance / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / RNA polymerase II promoter clearance / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / dephosphorylation / regulation of canonical Wnt signaling pathway / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / protein serine/threonine phosphatase activity / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / DARPP-32 events / transition metal ion binding / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / lung development / positive regulation of transcription elongation by RNA polymerase II / circadian regulation of gene expression / response to lead ion / regulation of circadian rhythm / : / presynapse / dendritic spine / perikaryon / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / 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
Chem-BKM / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.208 Å
AuthorsChoy, M.S. / Peti, W. / Page, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)GM098482 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)NS091336 United States
American Diabetes Association1-14-A-CN-31 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: PP1:Tautomycetin Complex Reveals a Path toward the Development of PP1-Specific Inhibitors.
Authors: Choy, M.S. / Swingle, M. / D'Arcy, B. / Abney, K. / Rusin, S.F. / Kettenbach, A.N. / Page, R. / Honkanen, R.E. / Peti, W.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)70,01413
Polymers68,3242
Non-polymers1,68911
Water5,188288
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0818
Polymers34,1621
Non-polymers9197
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9325
Polymers34,1621
Non-polymers7704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-75 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.199, 78.855, 133.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer as determined by gel filtration

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: residues 7-300
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

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Non-polymers , 5 types, 299 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BKM / (2Z)-2-[(1R)-3-{[(2R,3S,4R,7S,8S,11S,13R,16E)-17-ethyl-4,8-dihydroxy-3,7,11,13-tetramethyl-6,15-dioxononadeca-16,18-dien-2-yl]oxy}-1-hydroxy-3-oxopropyl]-3-methylbut-2-enedioic acid / Tautomycetin diacid form


Mass: 624.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H52O11
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 6000, 1 M lithium chloride, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→38.8222 Å / Num. obs: 35351 / % possible obs: 97.5 % / Redundancy: 7 % / Biso Wilson estimate: 36.82 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.047 / Rrim(I) all: 0.127 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.814 / Num. unique obs: 2260 / CC1/2: 0.503 / Rpim(I) all: 0.427 / Rrim(I) all: 0.927 / % possible all: 72.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
Aimless0.5.17data scaling
PHASER1.11.1phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 2.208→38.816 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 1795 5.11 %
Rwork0.1842 --
obs0.1858 35156 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.208→38.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 100 288 5052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024922
X-RAY DIFFRACTIONf_angle_d0.5626669
X-RAY DIFFRACTIONf_dihedral_angle_d7.5184015
X-RAY DIFFRACTIONf_chiral_restr0.038725
X-RAY DIFFRACTIONf_plane_restr0.003871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2075-2.26720.28761010.29871891X-RAY DIFFRACTION74
2.2672-2.33390.28641470.23542559X-RAY DIFFRACTION100
2.3339-2.40920.30091460.22592594X-RAY DIFFRACTION100
2.4092-2.49530.29891550.22172547X-RAY DIFFRACTION100
2.4953-2.59520.24531220.232600X-RAY DIFFRACTION100
2.5952-2.71330.27991360.22062616X-RAY DIFFRACTION100
2.7133-2.85630.25771410.21092603X-RAY DIFFRACTION100
2.8563-3.03520.23751460.20112602X-RAY DIFFRACTION100
3.0352-3.26940.23961400.19792589X-RAY DIFFRACTION100
3.2694-3.59820.21011540.17512608X-RAY DIFFRACTION100
3.5982-4.11840.21811180.15882685X-RAY DIFFRACTION100
4.1184-5.18680.13211390.13632672X-RAY DIFFRACTION100
5.1868-38.82220.18451500.17822795X-RAY DIFFRACTION100

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