[English] 日本語
Yorodumi
- PDB-1a17: TETRATRICOPEPTIDE REPEATS OF PROTEIN PHOSPHATASE 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a17
TitleTETRATRICOPEPTIDE REPEATS OF PROTEIN PHOSPHATASE 5
ComponentsSERINE/THREONINE PROTEIN PHOSPHATASE 5Serine/threonine-specific protein kinase
KeywordsHYDROLASE / PHOSPHATASE / PROTEIN-PROTEIN INTERACTIONS / TPR / SUPER-HELIX
Function / homology
Function and homology information


response to arachidonic acid / histone dephosphorylation / proximal dendrite / positive regulation of glucocorticoid receptor signaling pathway / peptidyl-threonine dephosphorylation / peptidyl-serine dephosphorylation / chaperone complex / protein serine/threonine phosphatase activity / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 ...response to arachidonic acid / histone dephosphorylation / proximal dendrite / positive regulation of glucocorticoid receptor signaling pathway / peptidyl-threonine dephosphorylation / peptidyl-serine dephosphorylation / chaperone complex / protein serine/threonine phosphatase activity / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / protein-serine/threonine phosphatase / G-protein alpha-subunit binding / phosphatase activity / phosphoprotein phosphatase activity / response to morphine / ESR-mediated signaling / ADP binding / protein dephosphorylation / negative regulation of protein phosphorylation / cellular response to cadmium ion / Hsp90 protein binding / negative regulation of neuron death / tau protein binding / response to lead ion / double-strand break repair / Negative regulation of MAPK pathway / MAPK cascade / cellular response to hydrogen peroxide / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic cell cycle / microtubule binding / positive regulation of I-kappaB kinase/NF-kappaB signaling / perikaryon / lipid binding / transcription, DNA-templated / intracellular membrane-bounded organelle / protein-containing complex binding / protein-containing complex / RNA binding / nucleoplasm / ATP binding / identical protein binding / plasma membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
Serine/threonine protein phosphatase 5 / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / PPP domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Calcineurin-like phosphoesterase domain, ApaH type ...Serine/threonine protein phosphatase 5 / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / PPP domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Tetratricopeptide repeat domain / Metallo-dependent phosphatase-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.45 Å
AuthorsDas, A.K. / Cohen, P.T.W. / Barford, D.
CitationJournal: EMBO J. / Year: 1998
Title: The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions.
Authors: Das, A.K. / Cohen, P.W. / Barford, D.
History
DepositionDec 23, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2533
Polymers19,0611
Non-polymers1922
Water1,40578
1
A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules

A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules

A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules

A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,01112
Polymers76,2424
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation16_665-y+3/2,-x+3/2,-z+1/21
MethodPQS
2
A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules

A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5056
Polymers38,1212
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
Buried area5090 Å2
ΔGint-87 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)90.060, 90.060, 104.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein SERINE/THREONINE PROTEIN PHOSPHATASE 5 / Serine/threonine-specific protein kinase / TETRATRICOPEPTIDE / TRP


Mass: 19060.549 Da / Num. of mol.: 1 / Fragment: PROTEIN INTERACTING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BRAIN / Gene: PPP5 / Plasmid: PT7.7 / Gene (production host): PPP5 / Production host: Escherichia coli (E. coli) / Strain (production host): PT7.7 / Tissue (production host): BRAIN
References: UniProt: P53041, protein-serine/threonine phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.5
Details: 1.8 M AMMONIUM SULFATE, 4% MPD, 100 MM HEPES PH 7.5, 2 MM DTT
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium salfate1reservoir
24 %(v/v)MPD1reservoir
3100 mMHEPES1reservoir
42 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.45→15 Å / Num. obs: 7832 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 24.4
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 3 / Rsym value: 0.133 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.82refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.45→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1045 13.4 %RANDOM
Rwork0.201 ---
obs0.201 7796 96.3 %-
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 10 78 1369
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH.WATER
X-RAY DIFFRACTION3PARAM.SULPHATETOP.SULPHATE
X-RAY DIFFRACTION4PARAM.SULPHATETOP.SULPHATE
Software
*PLUS
Name: X-PLOR / Version: 3.82 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.754

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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