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- PDB-5t58: Structure of the MIND Complex Shows a Regulatory Focus of Yeast K... -

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Basic information

Entry
Database: PDB / ID: 5t58
TitleStructure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly
Components
  • KLLA0C15939p
  • KLLA0D15741p
  • KLLA0E05809p
  • KLLA0F02343p
KeywordsCELL CYCLE / kinetochore / complex / chromosome / segregation / MIND / Mis12 / Mtw1 complex
Function / homology
Function and homology information


MIS12/MIND type complex / kinetochore assembly / mitotic sister chromatid segregation / chromosome segregation / cell division / nucleus
Similarity search - Function
Kinetochore-associated protein Nnf1 / Kinetochore Mis14/Nsl1 / Kinetochore protein Mis14 like / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family
Similarity search - Domain/homology
KLLA0F02343p / Kinetochore-associated protein / KLLA0D15741p / KLLA0C15939p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2131 Å
AuthorsDimitrova, Y. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C.
CitationJournal: Cell / Year: 2016
Title: Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly.
Authors: Dimitrova, Y.N. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Mar 6, 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: KLLA0F02343p
B: KLLA0E05809p
D: KLLA0D15741p
N: KLLA0C15939p


Theoretical massNumber of molelcules
Total (without water)104,2754
Polymers104,2754
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24340 Å2
ΔGint-198 kcal/mol
Surface area51820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.750, 172.570, 59.480
Angle α, β, γ (deg.)90.00, 110.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KLLA0F02343p


Mass: 27331.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue Ala0 is left over from the TEV cleavage site.
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_F02343g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CLK3
#2: Protein KLLA0E05809p


Mass: 23916.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_E05809g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CPD1
#3: Protein KLLA0D15741p


Mass: 27843.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_D15741g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CQN5
#4: Protein KLLA0C15939p


Mass: 25183.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_C15939g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CT27

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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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-Cl, pH 8.0, 18-22% PEG 550 MME, 0.5-4.5 % poly-gamma-glutamic acid low molecular weight (PGA-LM), 0.2 M potassium thiocyanate, 0.2 M potassium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.21→86.29 Å / Num. obs: 13484 / % possible obs: 74.4 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.207 / Net I/σ(I): 9.5
Reflection shellResolution: 3.21→3.33 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2131→86.285 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 44.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.362 677 5.02 %
Rwork0.3204 --
obs0.3225 13474 74.54 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2131→86.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6593 0 0 0 6593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036663
X-RAY DIFFRACTIONf_angle_d0.658966
X-RAY DIFFRACTIONf_dihedral_angle_d7.2145899
X-RAY DIFFRACTIONf_chiral_restr0.0371051
X-RAY DIFFRACTIONf_plane_restr0.0061150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2131-3.46120.5111300.4563631X-RAY DIFFRACTION18
3.4612-3.80960.46771050.37472056X-RAY DIFFRACTION60
3.8096-4.36080.37881850.33883190X-RAY DIFFRACTION94
4.3608-5.4940.40161700.31863457X-RAY DIFFRACTION100
5.494-86.31610.29371870.2893463X-RAY DIFFRACTION100

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