[English] 日本語
Yorodumi
- PDB-6zk6: Protein Phosphatase 1 (PP1) T320E mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zk6
TitleProtein Phosphatase 1 (PP1) T320E mutant
ComponentsSerine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / protein phosphatase 1 regulation / phosphorylation / phosphomimetic mutant
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 / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / response to lead ion / adherens junction / 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 / metal ion binding / 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 / 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: 1.9 Å
AuthorsSalvi, F. / Barabas, O. / Koehn, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)336567European Union
CitationJournal: Chembiochem / Year: 2021
Title: Towards Dissecting the Mechanism of Protein Phosphatase-1 Inhibition by Its C-Terminal Phosphorylation.
Authors: Salvi, F. / Hoermann, B. / Del Pino Garcia, J. / Fontanillo, M. / Derua, R. / Beullens, M. / Bollen, M. / Barabas, O. / Kohn, M.
History
DepositionJun 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0086
Polymers37,6911
Non-polymers3175
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-48 kcal/mol
Surface area11680 Å2
Unit cell
Length a, b, c (Å)38.546, 68.749, 127.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

-
Components

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


Mass: 37691.113 Da / Num. of mol.: 1 / Mutation: T320E
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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, TRIS , lithium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.9→36.22 Å / Num. obs: 26672 / % possible obs: 97.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.066 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1722 / CC1/2: 0.603 / Rpim(I) all: 0.433 / Rrim(I) all: 0.866 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G0J

6g0j


Resolution: 1.9→36.22 Å / SU ML: 0.1812 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1944 1286 4.83 %
Rwork0.1594 25351 -
obs0.1611 26637 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 9 128 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132355
X-RAY DIFFRACTIONf_angle_d1.1853192
X-RAY DIFFRACTIONf_chiral_restr0.0711346
X-RAY DIFFRACTIONf_plane_restr0.0064416
X-RAY DIFFRACTIONf_dihedral_angle_d21.0657855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.31661370.26362823X-RAY DIFFRACTION98.34
1.98-2.070.24751400.22172796X-RAY DIFFRACTION97.74
2.07-2.170.23131400.19122821X-RAY DIFFRACTION98.01
2.18-2.310.21871430.17672826X-RAY DIFFRACTION97.66
2.31-2.490.21911190.16872827X-RAY DIFFRACTION97.42
2.49-2.740.19261550.16782656X-RAY DIFFRACTION91.41
2.74-3.140.20651530.16312837X-RAY DIFFRACTION97.84
3.14-3.950.19731580.15022846X-RAY DIFFRACTION96.22
3.95-36.220.15751410.13642919X-RAY DIFFRACTION93.64
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.67446773158-3.05985195703-1.290947937724.429471318151.452013215765.559978656520.1581668479950.5487141637590.913921442723-0.822072531246-0.148957532125-0.721790702002-0.5944232984460.681549347244-0.006382919994120.5818636086430.1590212071550.1927685652040.6024046343840.2122214373330.46057413029487.726614412895.83732606751.51073621024
22.08147776007-0.0370143322278-0.6991068404934.23656202479-1.719467401272.887818127350.381572569011.098505701560.0152892834493-1.10487614639-0.05835923561371.064283538280.185156971278-0.294259472858-0.2591247584020.5196767435730.10776913772-0.1673021257870.6196416606470.02271636681390.4413738205372.438141658587.28245915133.28872251067
32.45969643854-0.773114010637-0.2274076438752.89162268902-0.1885107043052.479851795420.2299069685110.409084069320.169937484134-0.289668626394-0.256712219169-0.137296089369-0.08908117793420.09965919213940.04046481474470.2673204525480.03992216971720.02962181667170.3211067261780.05873470713770.24878896091282.466944688288.117142124612.6335821721
41.97107958484-0.5012114647720.3446761749112.2965216217-1.37407519542.527891790950.05011495929640.121479146947-0.0398510977464-0.233731368664-0.02221407449960.3570965250390.0871544024633-0.212099089458-0.001959486575210.2915661927290.0272594825246-0.01499362125250.3344020163980.02002894435070.31836195040174.47838718983.24297845714.8550807308
52.03653094345-0.967953869022-0.5155457181333.54008250822-0.8195072896972.20344672252-0.0406224718155-0.181337358617-0.1921067858270.43840570148-0.006679944608610.3222480155640.0701920692658-0.02041132931330.04540497418650.305380281394-0.002195802154340.05024793997290.2481481812330.03695982800360.29726854887776.150438027678.701474787229.6983900426
62.583471251110.980286963284-0.4926014222970.7921208450590.2071893664671.880087678370.0751049621814-0.5886746929160.1817737724570.810188204804-0.345529844311-0.866153939179-0.4823139988860.5542122530620.1693198960520.364001279336-0.0367345367282-0.08094343750010.3983301993670.03909155429790.43955052157890.94471587486.333772282627.7068009936
73.396240823191.57973845578-0.4698260944119.323001698380.6505431610763.630521831340.0627162625183-0.0110275612254-0.352268752693-0.187979583194-0.162358165336-1.345887248610.2727903112210.4552125131270.07980106226660.3061749362840.06623165665810.008536995325810.4233135246660.0661401885440.45155798725195.81121860777.834707182219.5529267768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 171 )
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 254 )
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 279 )
7X-RAY DIFFRACTION7chain 'A' and (resid 280 through 298 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more