[English] 日本語
Yorodumi
- PDB-5xw5: Crystal structure of budding yeast Cdc14p (C283S) bound to a Swi6... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xw5
TitleCrystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide
Components
  • Regulatory protein SWI6
  • Tyrosine-protein phosphatase CDC14
KeywordsCELL CYCLE / phosphatase
Function / homology
Function and homology information


SBF transcription complex / RENT complex / MBF transcription complex / positive regulation of mitotic actomyosin contractile ring assembly / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of reciprocal meiotic recombination / meiotic spindle disassembly / MAPK6/MAPK4 signaling / positive regulation of autophagosome assembly / protein tyrosine/serine/threonine phosphatase activity ...SBF transcription complex / RENT complex / MBF transcription complex / positive regulation of mitotic actomyosin contractile ring assembly / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of reciprocal meiotic recombination / meiotic spindle disassembly / MAPK6/MAPK4 signaling / positive regulation of autophagosome assembly / protein tyrosine/serine/threonine phosphatase activity / regulation of exit from mitosis / rDNA heterochromatin formation / autophagy of mitochondrion / cellular bud neck / cellular response to osmotic stress / spindle pole body / protein serine/threonine phosphatase activity / positive regulation of cytokinesis / phosphoprotein phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / chromosome segregation / G1/S transition of mitotic cell cycle / mitotic spindle / microtubule cytoskeleton organization / spindle pole / mitotic cell cycle / transcription coactivator activity / cell division / nucleolus / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Swi6, N-terminal / Swi6 N-terminal domain / Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. ...Swi6, N-terminal / Swi6 N-terminal domain / Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Ankyrin repeat / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Regulatory protein SWI6 / Tyrosine-protein phosphatase CDC14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsKobayashi, J. / Matsuura, Y.
CitationJournal: Protein Sci. / Year: 2017
Title: Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae
Authors: Kobayashi, J. / Matsuura, Y.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: 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: Tyrosine-protein phosphatase CDC14
B: Tyrosine-protein phosphatase CDC14
C: Regulatory protein SWI6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5944
Polymers96,4983
Non-polymers961
Water11,998666
1
A: Tyrosine-protein phosphatase CDC14
C: Regulatory protein SWI6


Theoretical massNumber of molelcules
Total (without water)48,8732
Polymers48,8732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-11 kcal/mol
Surface area16220 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase CDC14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7212
Polymers47,6251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-19 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.930, 95.930, 138.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Tyrosine-protein phosphatase CDC14


Mass: 47624.770 Da / Num. of mol.: 2 / Fragment: UNP residues 1-374 / Mutation: C283S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CDC14, OAF3, YFR028C / Production host: Escherichia coli (E. coli) / References: UniProt: Q00684, protein-tyrosine-phosphatase
#2: Protein/peptide Regulatory protein SWI6 / Cell-cycle box factor subunit SWI6 / MBF subunit P90 / Trans-acting activator of HO endonuclease gene


Mass: 1248.368 Da / Num. of mol.: 1 / Fragment: UNP residues 155-164 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09959
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Bis-Tris, ammonium sulfate, PEG 4000

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30.595 Å / Num. obs: 91878 / % possible obs: 97 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.033 / Rrim(I) all: 0.068 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.882.80.4420.8090.2920.53379.2
10.13-30.593.80.0190.9990.0110.02288.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XW4

5xw4


Resolution: 1.85→30.595 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.39
RfactorNum. reflection% reflection
Rfree0.2166 4595 5 %
Rwork0.1905 --
obs0.1918 91816 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.04 Å2 / Biso mean: 27.7239 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 1.85→30.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 5 666 6588
Biso mean--19.72 34.76 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066086
X-RAY DIFFRACTIONf_angle_d0.7588267
X-RAY DIFFRACTIONf_chiral_restr0.052885
X-RAY DIFFRACTIONf_plane_restr0.0051072
X-RAY DIFFRACTIONf_dihedral_angle_d2.943538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8710.30741070.2482308241578
1.871-1.8930.29321270.23672456258382
1.893-1.91610.29251250.22882531265685
1.9161-1.94040.26181450.20632601274688
1.9404-1.96590.22931260.19892727285392
1.9659-1.99280.22231450.18952857300296
1.9928-2.02130.20911570.18292938309598
2.0213-2.05150.21551680.176429183086100
2.0515-2.08350.21351600.17682942310299
2.0835-2.11770.19781620.17062943310599
2.1177-2.15420.19941450.1712971311699
2.1542-2.19330.1961650.16992937310299
2.1933-2.23550.20821650.16922953311899
2.2355-2.28110.19921320.16932980311299
2.2811-2.33070.18371640.16162946311099
2.3307-2.38490.19951520.16942974312699
2.3849-2.44450.21791560.17292964312099
2.4445-2.51060.22721630.17612955311899
2.5106-2.58440.21721850.172729743159100
2.5844-2.66780.2021370.173630043141100
2.6678-2.76310.22041450.178230073152100
2.7631-2.87360.25141520.181730093161100
2.8736-3.00430.18081750.181529963171100
3.0043-3.16250.20321730.189530073180100
3.1625-3.36050.19621580.18330243182100
3.3605-3.61950.22961390.192230513190100
3.6195-3.98310.20471590.194630353194100
3.9831-4.55780.2161760.199730533229100
4.5578-5.73620.22391610.21523025318698
5.7362-30.59910.24831710.22823135330697

+
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