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- PDB-2of3: TOG domain structure from C.elegans Zyg9 -

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Basic information

Entry
Database: PDB / ID: 2of3
TitleTOG domain structure from C.elegans Zyg9
ComponentsZYG-9
KeywordsSTRUCTURAL PROTEIN / CELL CYCLE / Multifunctional macromolecule / Kinetochore / microtubule / XMAP215 / Zyg9 / Stu2 / Dis1 / microtubule associated protein
Function / homology
Function and homology information


microtubule plus end polymerase / establishment or maintenance of microtubule cytoskeleton polarity / spindle elongation / meiotic spindle organization / meiotic spindle / embryo development ending in birth or egg hatching / spindle organization / microtubule polymerization / microtubule-based process / centrosome duplication ...microtubule plus end polymerase / establishment or maintenance of microtubule cytoskeleton polarity / spindle elongation / meiotic spindle organization / meiotic spindle / embryo development ending in birth or egg hatching / spindle organization / microtubule polymerization / microtubule-based process / centrosome duplication / mitotic spindle organization / kinetochore / spindle pole / microtubule binding / microtubule / cell division / centrosome / cytoplasm
Similarity search - Function
Zygote defective protein 9 / 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
Zygote defective protein 9 / :
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsAl-Bassam, J. / Larsen, N.A. / Hyman, A.A. / Harrison, S.C.
CitationJournal: Structure / Year: 2007
Title: Crystal structure of a TOG domain: conserved features of XMAP215/Dis1-family TOG domains and implications for tubulin binding.
Authors: Al-Bassam, J. / Larsen, N.A. / Hyman, A.A. / Harrison, S.C.
History
DepositionJan 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZYG-9


Theoretical massNumber of molelcules
Total (without water)30,0141
Polymers30,0141
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.130, 54.130, 116.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein ZYG-9 / Hypothetical protein zyg-9


Mass: 30013.926 Da / Num. of mol.: 1 / Fragment: TOG domain, residues 602-867
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zyg-9 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O61442, UniProt: G5EEM5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, 0.4 M NaCl, 2.0 M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97950, 0.97960, 0.92000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2005 / Details: Double Crystal Si(111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.921
ReflectionResolution: 1.9→50 Å / Num. all: 52652 / Num. obs: 38767 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Rmerge(I) obs: 0.053 / Rsym value: 0.061 / Net I/σ(I): 41.6
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.55 / Rsym value: 0.413 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.83 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.846 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22435 1335 5.1 %RANDOM
Rwork0.17294 ---
obs0.17548 25037 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.558 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 0 229 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222142
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.9852892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9545268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01125.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28415420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6971513
X-RAY DIFFRACTIONr_chiral_restr0.1440.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021544
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.21049
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21535
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2721.51381
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08822173
X-RAY DIFFRACTIONr_scbond_it3.5683848
X-RAY DIFFRACTIONr_scangle_it5.5164.5719
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 99 -
Rwork0.272 1851 -
obs--99.64 %

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