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- PDB-2qjx: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLI... -

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Basic information

Entry
Database: PDB / ID: 2qjx
TitleStructural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170 and EB1
ComponentsProtein BIM1
KeywordsPROTEIN BINDING / Calponin Homology Domain
Function / homology
Function and homology information


protein localization to microtubule plus-end / mitotic spindle orientation checkpoint signaling / thigmotropism / 2-micrometer plasmid partitioning / protein localization to microtubule / nuclear migration along microtubule / microtubule plus-end / negative regulation of microtubule depolymerization / microtubule plus-end binding / microtubule depolymerization ...protein localization to microtubule plus-end / mitotic spindle orientation checkpoint signaling / thigmotropism / 2-micrometer plasmid partitioning / protein localization to microtubule / nuclear migration along microtubule / microtubule plus-end / negative regulation of microtubule depolymerization / microtubule plus-end binding / microtubule depolymerization / microtubule organizing center / 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
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-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. ...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-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSlep, K.C. / Vale, R.D.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170, and EB1.
Authors: Slep, K.C. / Vale, R.D.
History
DepositionJul 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein BIM1


Theoretical massNumber of molelcules
Total (without water)15,1561
Polymers15,1561
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.849, 102.502, 31.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a dimer formed by a conserved coiled-coil / four helix bundle dimerization domain C-terminal to the calponin homology domain. The dimerization domain was not included in this crystallization construct.

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Components

#1: Protein Protein BIM1


Mass: 15155.825 Da / Num. of mol.: 1 / Fragment: Calponin Homology Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BIM1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P40013
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Tris, 200 mM Lithium sulfate, 29% PEG 4000, Protein stock 15 mg/ml, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97962, 0.97979, 1.03320
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 28, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979621
20.979791
31.03321
Reflection

D res high: 1.9 Å / D res low: 70 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
135.4791330.04111713298.6
233.2807150.0391.011736799.7
335.4753450.0341.021724598.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.097096.310.0381.002
3.254.0998.310.0371.023
2.843.2597.610.0391.018
2.582.8498.210.0421.008
2.392.5899.110.0470.983
2.252.3999.310.0510.966
2.142.2599.410.050.986
2.052.1499.510.0521.02
1.972.0599.410.0571.027
1.91.9798.510.0671.012
4.097098.420.0351.009
3.254.0999.720.0340.98
2.843.2510020.0370.994
2.582.8499.920.0391.048
2.392.5899.920.0441.031
2.252.3910020.050.953
2.142.2510020.050.961
2.052.1410020.0531.033
1.972.0510020.0611.032
1.91.9798.820.0751.044
4.097099.430.0311.03
3.254.0910030.0311.026
2.843.2510030.0331.014
2.582.8410030.0371.026
2.392.5810030.0431
2.252.3910030.0431.016
2.142.2510030.0451.026
2.052.1499.730.0521.046
1.972.0597.130.0581.049
1.91.9785.930.0681.045
ReflectionResolution: 1.9→70 Å / Num. obs: 17245 / % possible obs: 98.2 % / Rmerge(I) obs: 0.034 / Rsym value: 3.4 / Χ2: 1.024 / Net I/σ(I): 35.4
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 12.4 / Num. unique all: 1507 / Rsym value: 6.8 / Χ2: 1.045 / % possible all: 85.9

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Phasing

PhasingMethod: MAD
Phasing dm shellResolution: 1.9→500.01 Å / Delta phi final: 0.143 / FOM : 0.147 / Reflection: 17045

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MAD / Resolution: 1.9→33.84 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1629 9.3 %random 10%
Rwork0.193 ---
all-17572 --
obs-17045 97 %-
Solvent computationBsol: 41.405 Å2
Displacement parametersBiso mean: 22.183 Å2
Baniso -1Baniso -2Baniso -3
1--3.873 Å20 Å20 Å2
2--1.559 Å20 Å2
3---2.314 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 0 101 1092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.155
LS refinement shellResolution: 1.9→1.97 Å /
Rfactor% reflection
Rfree0.228 -
Rwork0.192 -
obs-85 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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