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- PDB-7don: Structure of tubulin H392D mutant from Odinarchaeota -

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Basic information

Entry
Database: PDB / ID: 7don
TitleStructure of tubulin H392D mutant from Odinarchaeota
ComponentsTubulin-like protein CetZ
KeywordsSTRUCTURAL PROTEIN / Asgard / tubulin / GTP / filament
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding
Similarity search - Function
Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain ...Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin-like protein CetZ
Similarity search - Component
Biological speciesOdinarchaeota archaeon
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRobinson, R.C. / Akil, C.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5 Japan
CitationJournal: To Be Published
Title: Structure of tubulin H392D mutant from Odinarchaeota
Authors: Robinson, R.C. / Akil, C.
History
DepositionDec 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.unpublished_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Tubulin-like protein CetZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6485
Polymers47,6331
Non-polymers1,0154
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-26 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.210, 92.614, 102.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tubulin-like protein CetZ


Mass: 47633.406 Da / Num. of mol.: 1 / Mutation: H392D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odinarchaeota archaeon (strain LCB_4) (archaea)
Strain: LCB_4 / Gene: cetZ, OdinLCB4_01330 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9N9N5
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGDP and GTP are in alternate conformations of each other
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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M Bis-Tris propane, pH 8.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.31 Å / Num. obs: 35951 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.87 Å / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3485 / CC1/2: 0.678 / Rpim(I) all: 0.464

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O2R

6o2r


Resolution: 1.8→46.31 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.208 -5 %
Rwork0.171 --
obs-35951 99.7 %
Displacement parametersBiso mean: 33.83 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 62 193 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01383542
X-RAY DIFFRACTIONf_angle_d1.28594833
X-RAY DIFFRACTIONf_chiral_restr0.078552
X-RAY DIFFRACTIONf_plane_restr0.0076611
X-RAY DIFFRACTIONf_dihedral_angle_d22.47861335

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