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- PDB-6fc5: Bik1 CAP-Gly domain -

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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


nuclear migration involved in conjugation with cellular fusion / 2-micrometer plasmid partitioning / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / cell tip / microtubule plus-end / microtubule plus-end binding / mating projection tip / spindle pole body / negative regulation of microtubule polymerization ...nuclear migration involved in conjugation with cellular fusion / 2-micrometer plasmid partitioning / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / cell tip / microtubule plus-end / microtubule plus-end binding / mating projection tip / spindle pole body / negative regulation of microtubule polymerization / microtubule associated complex / establishment of mitotic spindle orientation / cytoplasmic microtubule organization / kinetochore / spindle microtubule / spindle / cell cortex / microtubule binding / cell division / nucleus / cytoplasm
Similarity search - Function
CAP-Gly domain signature. / CAP_GLY / CAP-Gly domain profile. / CAP-Gly domain / CAP Gly-rich domain superfamily / CAP Gly-rich domain
Similarity search - Domain/homology
: / Nuclear fusion protein BIK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker'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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
γ
α
β
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

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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 (baker's yeast)
Gene: BIK1, SCKG_5419 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A250WN99, UniProt: P11709*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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 %

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