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- PDB-3woz: Crystal structure of CLASP2 TOG domain (TOG3) -

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Basic information

Entry
Database: PDB / ID: 3woz
TitleCrystal structure of CLASP2 TOG domain (TOG3)
ComponentsCLIP-associating protein 2
KeywordsSTRUCTURAL PROTEIN / HEAT Repeat / Microtubule binding / Tubulin / unknown / microtubule
Function / homology
Function and homology information


microtubule anchoring / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / microtubule organizing center organization / RHO GTPases Activate Formins / Separation of Sister Chromatids / fibroblast migration / negative regulation of microtubule depolymerization ...microtubule anchoring / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / microtubule organizing center organization / RHO GTPases Activate Formins / Separation of Sister Chromatids / fibroblast migration / negative regulation of microtubule depolymerization / microtubule nucleation / regulation of microtubule-based process / microtubule plus-end binding / microtubule depolymerization / exit from mitosis / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / cell leading edge / mitotic spindle organization / meiotic cell cycle / trans-Golgi network / kinetochore / microtubule cytoskeleton organization / ruffle membrane / spindle pole / cell migration / microtubule cytoskeleton / cell cortex / microtubule binding / microtubule / cell division / centrosome / Golgi apparatus / plasma membrane
Similarity search - Function
CLASP N-terminal domain / CLASP N terminal / Centrosomal protein CEP104-like, TOG domain / TOG domain / TOG / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
CLIP-associating protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsHayashi, I. / Maki, T.
CitationJournal: J. Mol. Biol. / Year: 2015
Title: CLASP2 Has Two Distinct TOG Domains That Contribute Differently to Microtubule Dynamics
Authors: Maki, T. / Grimaldi, A.D. / Fuchigami, S. / Kaverina, I. / Hayashi, I.
History
DepositionJan 6, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLIP-associating protein 2
B: CLIP-associating protein 2
C: CLIP-associating protein 2
D: CLIP-associating protein 2


Theoretical massNumber of molelcules
Total (without water)107,9054
Polymers107,9054
Non-polymers00
Water7,620423
1
A: CLIP-associating protein 2


Theoretical massNumber of molelcules
Total (without water)26,9761
Polymers26,9761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CLIP-associating protein 2


Theoretical massNumber of molelcules
Total (without water)26,9761
Polymers26,9761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CLIP-associating protein 2


Theoretical massNumber of molelcules
Total (without water)26,9761
Polymers26,9761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CLIP-associating protein 2


Theoretical massNumber of molelcules
Total (without water)26,9761
Polymers26,9761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.896, 122.317, 86.514
Angle α, β, γ (deg.)90.00, 94.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CLIP-associating protein 2 / Cytoplasmic linker-associated protein 2


Mass: 26976.156 Da / Num. of mol.: 4 / Fragment: UNP residues 642-873
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clasp2, Kiaa0627 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BRT1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 8
Details: 10mM Tris, 50mM NaCl, 2mM DTT, pH 8.0, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97893, 0.97921, 0.96399
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978931
20.979211
30.963991
ReflectionResolution: 2.2→50 Å / Num. obs: 56897 / % possible obs: 99.5 % / Observed criterion σ(F): 20.3 / Observed criterion σ(I): 2.6
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.18-2.22198.4
2.22-2.26199.9
2.26-2.31199.7
2.31-2.37199.7
2.37-2.42199.6
2.42-2.49199.8
2.49-2.56199.7
2.56-2.65199.7
2.65-2.74199.8
2.74-2.85199.8
2.85-2.98199.7
2.98-3.14199.8
3.14-3.33199.7
3.33-3.59199.5
3.59-3.95199.6
3.95-4.52199.3
4.52-5.7199.2
5.7-50197.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.186 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27941 2712 5.1 %RANDOM
Rwork0.24059 ---
obs0.24252 50760 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.379 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å2-0.64 Å2
2---2.2 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7270 0 0 423 7693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227429
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.97310032
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0695909
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98424.299335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.364151446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0921555
X-RAY DIFFRACTIONr_chiral_restr0.0570.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3691.54534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70727370
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07232895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.714.52657
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 203 -
Rwork0.287 3729 -
obs--100 %

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