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- PDB-4e61: Crystal structure of the EB1-like motif of Bim1p -

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Basic information

Entry
Database: PDB / ID: 4.0E+61
TitleCrystal structure of the EB1-like motif of Bim1p
ComponentsProtein BIM1
KeywordsCELL CYCLE / EB1-like motif / coiled-coil / spindle orientation / mitosis / Kar9p / phosphorylation / mitotic spindle / microtubules
Function / homology
Function and homology information


protein localization to microtubule plus-end / mitotic spindle orientation checkpoint signaling / 2-micrometer plasmid partitioning / protein localization to microtubule / nuclear migration along microtubule / microtubule plus-end / microtubule nucleation / negative regulation of microtubule depolymerization / microtubule plus-end binding / microtubule organizing center ...protein localization to microtubule plus-end / mitotic spindle orientation checkpoint signaling / 2-micrometer plasmid partitioning / protein localization to microtubule / nuclear migration along microtubule / microtubule plus-end / microtubule nucleation / negative regulation of microtubule depolymerization / microtubule plus-end binding / microtubule organizing center / microtubule depolymerization / mitotic sister chromatid cohesion / cytoplasmic microtubule / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / positive regulation of microtubule polymerization / mitotic spindle / spindle pole / cell division
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHuels, D. / Storchova, Z. / Niessing, D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Post-translational Modifications Regulate Assembly of Early Spindle Orientation Complex in Yeast.
Authors: Huls, D. / Storchova, Z. / Niessing, D.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein BIM1
B: Protein BIM1


Theoretical massNumber of molelcules
Total (without water)23,6162
Polymers23,6162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-46 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.000, 42.500, 100.500
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein BIM1


Mass: 11808.162 Da / Num. of mol.: 2
Fragment: C-terminal domain, EB1-like motif (UNP residues 182-282)
Source method: isolated from a genetically manipulated source
Details: Sequence GPLGS at the N-terminus is derived from expression vector
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BY4741 Mata / Gene: BIM1, YER016W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P40013

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Bis-Tris pH 8.0, 20% PEG 5000MME, 40% gamma-butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.25433 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2009
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25433 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 8938 / Num. obs: 8832 / % possible obs: 98.81 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 13.12
Reflection shellResolution: 2.45→2.59 Å / % possible all: 98.29

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Processing

Software
NameVersionClassification
XCUBEdata collection
SHELXCmodel building
SHELXDphasing
SHELXEmodel building
BUSTER-TNT2.Xrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Not fully refined model after structure determination by SAD with potassium tetranitroplatinate(II)-soaked crystals.

Resolution: 2.45→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2411 418 Random
Rwork0.2109 --
all0.2123 8937 -
obs-8832 -
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 0 0 1363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.18
X-RAY DIFFRACTIONt_bond_d0.098

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