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- PDB-8f8n: Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8f8n
TitleCrystal structure of the Arabidopsis SPIRAL2 C-terminal domain
ComponentsMicrotubule-associated protein TORTIFOLIA1
KeywordsSTRUCTURAL PROTEIN / Microtubule Regulator / Microtubule Minus-End Binding Protein / Katanin p80-Like domain
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 / Microtubule-associated protein TORTIFOLIA1
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.798 Å
AuthorsSlep, K.C. / Bolhuis, D.B. / Dixit, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008570 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM139552 United States
CitationJournal: Plos One / Year: 2023
Title: Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain.
Authors: Bolhuis, D.L. / Dixit, R. / Slep, K.C.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated protein TORTIFOLIA1


Theoretical massNumber of molelcules
Total (without water)24,5921
Polymers24,5921
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, monomer as assayed using SECMALS, gel filtration, monomer as assayed using SECMALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.480, 47.732, 111.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24592.164 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 / Plasmid: pET-28
Details (production host): N-term His tag, thrombin cleavage site
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9T041
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Well solution (1ml) = 1.05 M Ammonium sulfate, 100 mM sodium acetate pH 4.6 Protein solution = 7 mg/ml protein in 25 mM Tris pH 8.5, 500 mM NaCl, and 0.1% beta-mercaptoethanol, 5 mM L- ...Details: Well solution (1ml) = 1.05 M Ammonium sulfate, 100 mM sodium acetate pH 4.6 Protein solution = 7 mg/ml protein in 25 mM Tris pH 8.5, 500 mM NaCl, and 0.1% beta-mercaptoethanol, 5 mM L-methionine Hanging drop = 2+2 microliters

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792603 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792603 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 33280 / % possible obs: 98 % / Redundancy: 5.6 % / CC1/2: 0.994 / CC star: 0.994 / Rmerge(I) obs: 0.098 / Χ2: 0.028 / Net I/av σ(I): 21.8 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.863.20.19431580.63192.1
1.86-1.9440.1533110.742198.8
1.94-2.0360.12433730.8251100
2.03-2.136.80.10334320.8641100
2.13-2.276.80.08833900.836199.9
2.27-2.446.30.07633720.822199.9
2.44-2.6960.06934030.774199.6
2.69-3.086.30.06233640.81199.1
3.08-3.885.20.05232280.807195.1
3.88-505.60.0532490.716195.1

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.798→33.799 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.58 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2171 1792 10 %
Rwork0.1859 --
obs0.189 17913 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.798→33.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 0 95 1268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111199
X-RAY DIFFRACTIONf_angle_d1.3231636
X-RAY DIFFRACTIONf_dihedral_angle_d15.612435
X-RAY DIFFRACTIONf_chiral_restr0.079183
X-RAY DIFFRACTIONf_plane_restr0.006215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.84620.28241230.20851113X-RAY DIFFRACTION90
1.8462-1.90050.23971350.19991205X-RAY DIFFRACTION97
1.9005-1.96180.25631360.18711231X-RAY DIFFRACTION99
1.9618-2.03190.22321370.18361231X-RAY DIFFRACTION100
2.0319-2.11330.22651390.18541249X-RAY DIFFRACTION100
2.1133-2.20940.20921400.17441256X-RAY DIFFRACTION100
2.2094-2.32590.18791380.17921245X-RAY DIFFRACTION100
2.3259-2.47160.22821380.18141249X-RAY DIFFRACTION100
2.4716-2.66230.21921400.17951257X-RAY DIFFRACTION100
2.6623-2.93010.22691400.19561260X-RAY DIFFRACTION99
2.9301-3.35380.24491400.20011259X-RAY DIFFRACTION99
3.3538-4.22410.1931370.17681227X-RAY DIFFRACTION95
4.2241-33.7990.20521490.18571339X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 30.0428 Å / Origin y: 16.0506 Å / Origin z: 40.9647 Å
111213212223313233
T0.131 Å20.0146 Å2-0.01 Å2-0.133 Å2-0.0018 Å2--0.1586 Å2
L1.7911 °20.7668 °2-1.6845 °2-1.2971 °2-1.1825 °2--3.3579 °2
S0.0485 Å °-0.0038 Å °0.1739 Å °-0.0149 Å °0 Å °0.0025 Å °-0.2284 Å °-0.031 Å °-0.0302 Å °
Refinement TLS groupSelection details: all

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