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- PDB-8d00: Structure of the Arabidopsis thaliana SPIRAL2 TOG domain -

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Basic information

Entry
Database: PDB / ID: 8d00
TitleStructure of the Arabidopsis thaliana SPIRAL2 TOG domain
ComponentsMicrotubule-associated protein TORTIFOLIA1
KeywordsSTRUCTURAL PROTEIN / TOG / HEAT / Alpha-solenoid / Microtubule-binding
Function / homologycortical microtubule, transverse to long axis / circumnutation / MT-associated protein TORTIFOLIA1/SPIRAL2-like / unidimensional cell growth / Armadillo-like helical / microtubule binding / Armadillo-type fold / IODIDE ION / Microtubule-associated protein TORTIFOLIA1
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSlep, K.C. / Bolhuis, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
University of North Carolina Ralph W. Mosley Fund United States
CitationJournal: Plant Cell / Year: 2023
Title: A structurally divergent TOG domain stabilizes microtubule minus ends in Arabidopsis
Authors: Fan, Y. / Bilkey, N. / Bolhuis, D.L. / Slep, K.C. / Dixit, R.
History
DepositionMay 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated protein TORTIFOLIA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0472
Polymers32,9201
Non-polymers1271
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer by SECMALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-0 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.843, 78.456, 131.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Microtubule-associated protein TORTIFOLIA1 / Microtubule-associated protein SPIRAL2 / Protein CONVOLUTA


Mass: 32920.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TOR1, CN, SPR2, At4g27060, T24A18.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9T041
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.25 % / Description: rods 50 x 50 x 400 microns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2 ul 15.7 mg/mL SPIRAL2 TOG domain (residues 33-333) protein + 2 ul of a 1 ml well solution (27.5% w/v PEG3350, 150 mM ammonium phosphate, 280 mM sodium iodide)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021
RadiationMonochromator: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9490 / % possible obs: 98.7 % / Redundancy: 11.5 % / Biso Wilson estimate: 58.9 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rsym value: 0.164 / Net I/σ(I): 19.7
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 944 / CC1/2: 0.872 / CC star: 0.965 / Rsym value: 0.842

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold prediction

Resolution: 2.8→38.36 Å / SU ML: 0.3475 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 26.7654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 917 10.01 %
Rwork0.2138 8246 -
obs0.2184 9163 95.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.99 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 1 7 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032288
X-RAY DIFFRACTIONf_angle_d0.53543091
X-RAY DIFFRACTIONf_chiral_restr0.0362378
X-RAY DIFFRACTIONf_plane_restr0.0047384
X-RAY DIFFRACTIONf_dihedral_angle_d14.232856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.34451130.27561078X-RAY DIFFRACTION89.89
2.95-3.130.4081230.27451098X-RAY DIFFRACTION89.45
3.13-3.370.28551290.2541157X-RAY DIFFRACTION95.9
3.37-3.710.25351340.22151205X-RAY DIFFRACTION97.67
3.71-4.250.26111390.20641221X-RAY DIFFRACTION98.55
4.25-5.350.22681310.19091205X-RAY DIFFRACTION96.46
5.35-38.360.22881480.19251282X-RAY DIFFRACTION97.95
Refinement TLS params.Method: refined / Origin x: -9.79538249122 Å / Origin y: -5.82707630509 Å / Origin z: -41.1953209771 Å
111213212223313233
T0.228642178596 Å2-0.028372723038 Å2-0.00020622167415 Å2-0.169466859148 Å20.0206098235539 Å2--0.201030932884 Å2
L1.90217913262 °2-0.637742860724 °20.546585747629 °2-0.366357534206 °2-0.19869684322 °2--0.645815103951 °2
S-0.0662388110553 Å °-0.0523822532602 Å °-0.0837625443668 Å °0.0725670527552 Å °0.0189834631742 Å °0.0776669699468 Å °0.071164876276 Å °-0.0262305231103 Å °-0.000758518155616 Å °
Refinement TLS groupSelection details: all

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