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- PDB-2ftx: Crystal structure of the yeast kinetochore Spc24/Spc25 globular domain -

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Basic information

Entry
Database: PDB / ID: 2ftx
TitleCrystal structure of the yeast kinetochore Spc24/Spc25 globular domain
Components
  • Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region
  • Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region
Keywordsstructural protein / protein binding / alpha-beta / complex / coiled-coil
Function / homology
Function and homology information


centromere clustering / Ndc80 complex / sister chromatid biorientation / chromosome segregation / kinetochore / cell division / identical protein binding / nucleus
Similarity search - Function
Double Stranded RNA Binding Domain - #430 / Chromosome segregation protein Spc25 / Spc24, Fungi, globular domain superfamily / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Kinetochore protein SPC25 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsWei, R.R. / Harrison, S.C.
CitationJournal: To be Published
Title: Atomic Structure of the kinetochore Spc24p/Spc25p globular domain reveals a novel fold
Authors: Wei, R.R. / Harrison, S.C. / Schnell, J.R. / Chou, J.J.
History
DepositionJan 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region
B: Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6804
Polymers17,5622
Non-polymers1182
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-36 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.907, 84.907, 93.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region


Mass: 10029.981 Da / Num. of mol.: 1 / Fragment: Spc25p globular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YER018C / Plasmid: pET3aTr / Cell line (production host): Rosetta / Production host: Escherichia coli (E. coli) / References: UniProt: P40014
#2: Protein Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region


Mass: 7532.432 Da / Num. of mol.: 1 / Fragment: Spc24p globular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YMR117C, YM9718.16C / Plasmid: pET3aTr / Cell line (production host): Rosetta / Production host: Escherichia coli (E. coli) / References: UniProt: Q04477
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 293 K / pH: 10.5
Details: 0.1 M CAPS, pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 10.50

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97950, 0.97967, 0.953725
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979671
30.9537251
ReflectionResolution: 1.9→50 Å / Num. obs: 13528 / % possible obs: 98 % / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.97 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.096 / SU ML: 0.092 / σ(F): 2 / ESU R: 0.161 / ESU R Free: 0.136 / Stereochemistry target values: ENGH & HUBER / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 685 -RANDOMLY SELECTED
Rwork0.209 ---
obs0.21 12988 99.8 %-
all-13014 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.377 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---0.64 Å20 Å2
3---1.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.136 Å0.161 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 6 79 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221205
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9721633
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9255147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91124.40759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3215212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02899
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2500
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2806
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2111.5739
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16221186
X-RAY DIFFRACTIONr_scbond_it2.8513478
X-RAY DIFFRACTIONr_scangle_it4.464.5447
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.252 63 -
Rwork0.22 --
obs--97.4 %

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