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- PDB-2qk2: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLI... -

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Basic information

Entry
Database: PDB / ID: 2qk2
TitleStructural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170 and EB1
ComponentsLP04448p
KeywordsPROTEIN BINDING / Mini spindles / Msps / XMAP215 / Dis1 / Stu2 / HEAT repeat / microtubule plus end / +TIP
Function / homology
Function and homology information


establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / microtubule plus-end / female meiotic nuclear division / positive regulation of microtubule nucleation ...establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / microtubule plus-end / female meiotic nuclear division / positive regulation of microtubule nucleation / microtubule plus-end binding / endoplasmic reticulum organization / oogenesis / microtubule polymerization / establishment of mitotic spindle orientation / centrosome duplication / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / axon guidance / spindle / kinetochore / spindle pole / mitotic cell cycle / microtubule binding / centrosome / cytoplasm
Similarity search - Function
XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant ...XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein mini spindles / Protein mini spindles
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 10, 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

Downloads & links

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Assembly

Deposited unit
A: LP04448p


Theoretical massNumber of molelcules
Total (without water)26,7631
Polymers26,7631
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.370, 113.414, 78.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsMsps is a monomer. The N-terminal two-thirds is characterized by five arrayed TOG domains. This structure is the second of the five TOG domains.

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Components

#1: Protein LP04448p


Mass: 26762.619 Da / Num. of mol.: 1 / Fragment: TOG domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: msps / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: Q4QQC0, UniProt: Q9VEZ3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.8 Å3/Da / Density % sol: 67.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.25 M Sodium malonate, Protein concentration 15 mg/ml , pH 7.0, 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: 0.97963, 0.97974, 1.00801
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
10.979631
20.979741
31.008011
Reflection

D res high: 2.1 Å / D res low: 70 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
1161364710.0390.944486097.5
216.51383780.0380.944538598.6
317.91376770.0350.964514998.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.527088.110.0190.958
3.594.5296.910.0221.036
3.143.5998.710.0291.049
2.853.1499.110.0431.026
2.652.8599.210.0620.978
2.492.6599.210.0870.935
2.372.4999.210.1040.862
2.262.3799.110.1440.866
2.182.269910.1930.863
2.12.1896.510.240.816
4.527095.720.0180.966
3.594.5299.220.0221.042
3.143.5999.420.0291.041
2.853.1499.520.0421.031
2.652.8599.520.0610.987
2.492.6599.220.0830.919
2.372.4999.220.1020.898
2.262.379920.1390.849
2.182.269920.1820.821
2.12.1896.420.2290.786
4.52709730.0170.953
3.594.5299.330.0211.034
3.143.5999.430.0271.042
2.853.1499.630.0391.032
2.652.8599.230.0551.02
2.492.6599.130.0760.986
2.372.4999.330.0910.946
2.262.3799.130.1240.875
2.182.2698.430.1640.868
2.12.1891.630.1850.779
ReflectionResolution: 2.1→70 Å / Num. obs: 45149 / % possible obs: 98.2 % / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Χ2: 0.961 / Net I/σ(I): 17.9
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.3 / Num. unique all: 4223 / Rsym value: 0.185 / Χ2: 0.779 / % possible all: 91.6

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Phasing

PhasingMethod: MAD
Phasing dm shellResolution: 2.1→500.01 Å / Delta phi final: 0.153 / FOM : 0.156 / Reflection: 43880

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MAD / Resolution: 2.1→35.58 Å / FOM work R set: 0.868 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4291 9.3 %Random 10%
Rwork0.202 ---
obs-43880 95.3 %-
Solvent computationBsol: 55.201 Å2
Displacement parametersBiso mean: 33.672 Å2
Baniso -1Baniso -2Baniso -3
1--7.726 Å20 Å20 Å2
2--5.267 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 0 161 2012
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3821.5
X-RAY DIFFRACTIONc_scbond_it2.7242
X-RAY DIFFRACTIONc_mcangle_it2.1152
X-RAY DIFFRACTIONc_scangle_it4.1182.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.110.23700.238587657
2.11-2.130.237870.231673760
2.13-2.140.244900.242721811
2.14-2.160.339790.239656735
2.16-2.180.254860.221726812
2.18-2.190.287670.252774841
2.19-2.210.274680.237755823
2.21-2.230.2821090.224774883
2.23-2.240.244750.225754829
2.24-2.260.287790.232752831
2.26-2.280.238660.21825891
2.28-2.30.211840.218767851
2.3-2.320.279840.219791875
2.32-2.340.25760.218796872
2.34-2.370.241790.228802881
2.37-2.390.258810.211785866
2.39-2.410.208890.209799888
2.41-2.440.229840.218833917
2.44-2.460.312830.227773856
2.46-2.490.223990.211794893
2.49-2.520.221020.211796898
2.52-2.550.281790.233816895
2.55-2.580.244720.233801873
2.58-2.610.31850.234836921
2.61-2.650.265930.233769862
2.65-2.680.206820.235846928
2.68-2.720.317450.234833878
2.72-2.760.213970.247816913
2.76-2.80.249930.234818911
2.8-2.850.34870.224785872
2.85-2.90.23990.238835934
2.9-2.950.212830.234804887
2.95-3.010.245960.232817913
3.01-3.070.212780.228817895
3.07-3.140.239990.223832931
3.14-3.210.201930.227798891
3.21-3.290.221770.185838915
3.29-3.380.269780.202844922
3.38-3.480.261660.183845911
3.48-3.590.182850.176829914
3.59-3.720.152840.168820904
3.72-3.870.1531030.145821924
3.87-4.040.145990.165816915
4.04-4.260.193960.162808904
4.26-4.520.1631030.158820923
4.52-4.870.167980.164822920
4.87-5.360.163840.192817901
5.36-6.140.223930.215785878
6.14-7.740.2681020.2801903
7.74-500.010.231050.186767872
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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