[English] 日本語
Yorodumi
- PDB-1sw6: S. CEREVISIAE SWI6 ANKYRIN-REPEAT FRAGMENT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sw6
TitleS. CEREVISIAE SWI6 ANKYRIN-REPEAT FRAGMENT
ComponentsREGULATORY PROTEIN SWI6
KeywordsTRANSCRIPTION REGULATION / ANKYRIN REPEATS / CELL-CYCLE
Function / homology
Function and homology information


SBF transcription complex / MBF transcription complex / positive regulation of reciprocal meiotic recombination / G1/S transition of mitotic cell cycle / transcription coactivator activity / 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 / Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Swi6, N-terminal / Swi6 N-terminal domain / Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein SWI6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsFoord, R. / Taylor, I.A. / Sedgwick, S.G. / Smerdon, S.J.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: X-ray structural analysis of the yeast cell cycle regulator Swi6 reveals variations of the ankyrin fold and has implications for Swi6 function.
Authors: Foord, R. / Taylor, I.A. / Sedgwick, S.G. / Smerdon, S.J.
History
DepositionSep 28, 1998Processing site: BNL
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REGULATORY PROTEIN SWI6
B: REGULATORY PROTEIN SWI6


Theoretical massNumber of molelcules
Total (without water)72,2422
Polymers72,2422
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.850, 91.730, 90.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.790696, -0.605652, 0.089357), (-0.556889, -0.772177, -0.305968), (0.25431, 0.192166, -0.947839)
Vector: 43.38985, 95.3136, 15.6829)

-
Components

#1: Protein REGULATORY PROTEIN SWI6


Mass: 36121.246 Da / Num. of mol.: 2 / Fragment: ANKYRIN-REPEAT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SWI6 / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P09959
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / PH range low: 8.7 / PH range high: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
224-27 %PEG33501reservoir
350 mMTris-HCl1reservoir
4300 mM1reservoirNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.9, 0.9795, 0.9799
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97951
30.97991
ReflectionResolution: 3.5→20 Å / Num. obs: 8625 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 12
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / Redundancy: 6.5 %

-
Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 -5 %RANDOM
Rwork0.222 ---
obs0.222 30610 86 %-
Displacement parametersBiso mean: 42.14 Å2
Baniso -1Baniso -2Baniso -3
1-5.72 Å20 Å20 Å2
2---12.783 Å20 Å2
3---7.064 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 0 215 4155
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.462.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.226 / Rfactor Rfree: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg2.1

+
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