[English] 日本語
Yorodumi
- PDB-6fc5: Bik1 CAP-Gly domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fc5
TitleBik1 CAP-Gly domain
ComponentsMicrotubule-associated protein
KeywordsCELL CYCLE / +TIP / CAP-Gly / microtubule / yeast
Function / homology
Function and homology information


protein localization to mitotic spindle pole body / nuclear migration involved in conjugation with cellular fusion / 2-micrometer plasmid partitioning / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / sister chromatid segregation / cell tip / microtubule plus-end / microtubule nucleation / mating projection tip ...protein localization to mitotic spindle pole body / nuclear migration involved in conjugation with cellular fusion / 2-micrometer plasmid partitioning / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / sister chromatid segregation / cell tip / microtubule plus-end / microtubule nucleation / mating projection tip / spindle pole body / microtubule associated complex / negative regulation of microtubule polymerization / establishment of mitotic spindle orientation / kinesin binding / spindle microtubule / kinetochore / spindle / cell cortex / microtubule binding / cell division
Similarity search - Function
CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY
Similarity search - Domain/homology
: / Nuclear fusion protein BIK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsKumar, A. / Stangier, M.M. / Steinmetz, M.O.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
SystemsX.chRTD-TubeX Switzerland
Marie CurieCOFUND fellowship Switzerland
CitationJournal: Structure / Year: 2018
Title: Structure-Function Relationship of the Bik1-Bim1 Complex.
Authors: Stangier, M.M. / Kumar, A. / Chen, X. / Farcas, A.M. / Barral, Y. / Steinmetz, M.O.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)11,3571
Polymers11,3571
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.663, 53.663, 61.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Microtubule-associated protein


Mass: 11357.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GPMDRYQRKIGCFIQIPNLGRGQLKYVGPVDTKAGMFAGVDLLANIGKNDGSFMGKKYFQTE YPQSGLFIQLQKVASLIEKASISQTSRRTTMEPLSIPKNR
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BIK1, SCKG_5419 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A250WN99, UniProt: P11709*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M sodium cacodylate, 1.0 M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→40.4 Å / Num. obs: 7731 / % possible obs: 99.8 % / Redundancy: 25 % / Net I/σ(I): 28.2
Reflection shellResolution: 1.88→1.95 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→40.4 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.737 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 769 10 %RANDOM
Rwork0.1669 ---
obs0.1698 6923 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.45 Å2 / Biso mean: 34.056 Å2 / Biso min: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.53 Å2
Refinement stepCycle: final / Resolution: 1.88→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms650 0 0 48 698
Biso mean---40.59 -
Num. residues----84
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019662
X-RAY DIFFRACTIONr_bond_other_d0.0020.02639
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.977885
X-RAY DIFFRACTIONr_angle_other_deg1.08631488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.11324.64328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52815123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.877153
X-RAY DIFFRACTIONr_chiral_restr0.1190.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02727
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02132
LS refinement shellResolution: 1.883→1.931 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 54 -
Rwork0.259 491 -
all-545 -
obs--97.32 %

+
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