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- PDB-7ag9: Structure of the Kar9 protein -

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Basic information

Entry
Database: PDB / ID: 7ag9
TitleStructure of the Kar9 protein
ComponentsKar9
KeywordsCELL CYCLE / Cytoskeleton / Cell Division / Microtubules
Function / homology
Function and homology information


mitotic spindle orientation checkpoint signaling / kinetochore => GO:0000776 / establishment of spindle localization / nuclear migration along microtubule / mating projection tip / spindle pole body / cytoplasmic microtubule / cell cortex
Similarity search - Function
Karyogamy protein, KAR9 / Yeast cortical protein KAR9
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesNaumovozyma castellii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsKumar, A. / prota, A.E. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Structure / Year: 2021
Title: Structure of the Kar9 protein
Authors: Kumar, A. / Steinmetz, M.O.
History
DepositionSep 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kar9
B: Kar9


Theoretical massNumber of molelcules
Total (without water)100,5822
Polymers100,5822
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, MALS and mutational analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-7 kcal/mol
Surface area41790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.621, 125.621, 165.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Kar9


Mass: 50291.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naumovozyma castellii (strain ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630) (fungus)
Strain: ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630 / Gene: NCAS0D02220, NCAS_0D02220 / Production host: Escherichia coli (E. coli) / References: UniProt: G0VE12

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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: 6.48 Å3/Da / Density % sol: 81.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM Tris-HCl, pH 7.5, 500 mM NaCl supplemented with 250 mM gamma amino butyric acid (GABA).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50.01 Å / Num. obs: 38506 / % possible obs: 99.8 % / Redundancy: 12.3 % / CC1/2: 0.999 / Net I/σ(I): 11.09
Reflection shellResolution: 3.3→3.4 Å / Num. unique obs: 12118 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→46.86 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 28.741 / SU ML: 0.442 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.625 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2574 6.7 %RANDOM
Rwork0.2643 ---
obs0.2659 35932 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 306.78 Å2 / Biso mean: 144.18 Å2 / Biso min: 83.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å20 Å20 Å2
2---2.34 Å20 Å2
3---4.68 Å2
Refinement stepCycle: final / Resolution: 3.3→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5948 0 0 0 5948
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136041
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175802
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.6328196
X-RAY DIFFRACTIONr_angle_other_deg1.1841.5813297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2365754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66424.459305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.553151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9741526
X-RAY DIFFRACTIONr_chiral_restr0.0570.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021308
LS refinement shellResolution: 3.301→3.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 198 -
Rwork0.396 2599 -
all-2797 -
obs--99.57 %

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