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- PDB-6gdj: Crystal structure of Mto2 twin-cysteine dimerisation domain -

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Basic information

Entry
Database: PDB / ID: 6gdj
TitleCrystal structure of Mto2 twin-cysteine dimerisation domain
ComponentsMto2
KeywordsSTRUCTURAL PROTEIN / Microtubule organisation Microtubule nucleation
Function / homology
Function and homology information


interphase microtubule organizing center assembly / static microtubule bundle / equatorial microtubule organizing center / mitotic spindle pole body / interphase microtubule organizing center / microtubule bundle formation / nuclear migration / cell division site / mitotic cytokinesis / cytoplasmic microtubule ...interphase microtubule organizing center assembly / static microtubule bundle / equatorial microtubule organizing center / mitotic spindle pole body / interphase microtubule organizing center / microtubule bundle formation / nuclear migration / cell division site / mitotic cytokinesis / cytoplasmic microtubule / microtubule cytoskeleton / cytosol / cytoplasm
Similarity search - Function
Gamma tubulin complex adapter mto2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsThakur, H.C. / Sawin, K.E. / Cook, A.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust094517/z/10/z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of Mto2 twin-cysteine dimerisation domain
Authors: Thakur, H.C. / Sawin, K.E. / Cook, A.G.
History
DepositionApr 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: 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: Mto2
B: Mto2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9484
Polymers18,7632
Non-polymers1842
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, dilution ITC does not dissociate this dimer, gel filtration, SEC-MALS data indicate that this molecule is a homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-24 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.704, 73.704, 54.363
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Mto2


Mass: 9381.744 Da / Num. of mol.: 2 / Fragment: twin-cysteine dimerisation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPBC902.06 / Plasmid: pGGWA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RILP / References: UniProt: Q9USP7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 10-22% PEG 3350, 0.2M sodium acetate trihydrate or sodium thiocyanate pH6-7
PH range: 6-7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0211
SYNCHROTRONDiamond I0420.979
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELOct 8, 2014
DECTRIS PILATUS3 S 6M2PIXELFeb 7, 2015
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double CrystalSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
ReflectionResolution: 1.5→41.39 Å / Num. obs: 26976 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.078 / Rrim(I) all: 0.173 / Net I/σ(I): 6.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3891 / CC1/2: 0.92 / Rpim(I) all: 0.226 / Rrim(I) all: 0.509 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSNovember 3, 2014data reduction
SCALA3.3.16data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→41.39 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.313 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18317 1261 4.7 %RANDOM
Rwork0.15233 ---
obs0.1538 25696 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.24 Å20 Å2
2---0.47 Å20 Å2
3---1.53 Å2
Refinement stepCycle: 1 / Resolution: 1.5→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 12 56 1095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191060
X-RAY DIFFRACTIONr_bond_other_d0.0010.021040
X-RAY DIFFRACTIONr_angle_refined_deg1.8042.0071451
X-RAY DIFFRACTIONr_angle_other_deg1.08932410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1495140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0092430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.58215172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.306156
X-RAY DIFFRACTIONr_chiral_restr0.1280.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211133
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02169
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_it2.3762.148563
X-RAY DIFFRACTIONr_mcbond_other2.2922.142562
X-RAY DIFFRACTIONr_mcangle_it2.7833.209702
X-RAY DIFFRACTIONr_mcangle_other2.7953.214703
X-RAY DIFFRACTIONr_scbond_it3.7082.477497
X-RAY DIFFRACTIONr_scbond_other3.6942.476497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3273.608750
X-RAY DIFFRACTIONr_long_range_B_refined3.76728.4021208
X-RAY DIFFRACTIONr_long_range_B_other3.76628.4421209
X-RAY DIFFRACTIONr_rigid_bond_restr3.97832100
X-RAY DIFFRACTIONr_sphericity_free19.413541
X-RAY DIFFRACTIONr_sphericity_bonded9.99852100
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 82 -
Rwork0.202 1886 -
obs--99.6 %

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