[English] 日本語
Yorodumi
- PDB-1wao: PP5 structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wao
TitlePP5 structure
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 / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity ...response to arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / ESR-mediated signaling / protein dephosphorylation / ADP binding / response to lead ion / Hsp90 protein binding / tau protein binding / Negative regulation of MAPK pathway / double-strand break repair / MAPK cascade / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / DNA-templated transcription / lipid binding / protein-containing complex / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / 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 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat ...PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / 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 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBarford, D.
CitationJournal: Embo J. / Year: 2005
Title: Molecular Basis for Tpr Domain-Mediated Regulation of Protein Phosphatase 5
Authors: Yang, J. / Roe, S.M. / Cliff, M.J. / Williams, M.A. / Ladbury, J.E. / Cohen, P.T. / Barford, D.
History
DepositionOct 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: SERINE/THREONINE PROTEIN PHOSPHATASE 5
2: SERINE/THREONINE PROTEIN PHOSPHATASE 5
3: SERINE/THREONINE PROTEIN PHOSPHATASE 5
4: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,70712
Polymers218,2684
Non-polymers4408
Water0
1
1: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6773
Polymers54,5671
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
2: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6773
Polymers54,5671
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
3: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6773
Polymers54,5671
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
4: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6773
Polymers54,5671
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.740, 117.540, 200.410
Angle α, β, γ (deg.)90.00, 93.79, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
SERINE/THREONINE PROTEIN PHOSPHATASE 5 / Serine/threonine-specific protein kinase / PP5 / PROTEIN PHOSPHATASE T / PP-T / PPT / PROTEIN PHOSPHATASE 5


Mass: 54566.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL834
References: UniProt: P53041, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
Compound detailsCATALYTIC ACTIVITY: PHOSPHOPROTEIN + H2O = PROTEIN + PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 50 %
Crystal growDetails: PEG 6K 10%

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 53119 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 102.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.4
Reflection shellResolution: 2.9→3.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→33.78 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1676595.08 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1319 2.5 %RANDOM
Rwork0.247 ---
obs0.247 53095 99 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 40.0415 Å2 / ksol: 0.270929 e/Å3
Displacement parametersBiso mean: 98.43 Å2
Baniso -1Baniso -2Baniso -3
1-26.7 Å20 Å2-12.96 Å2
2--1.09 Å20 Å2
3----27.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.9→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15074 0 8 0 15082
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.375
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellHighest resolution: 2.9 Å

+
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