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- PDB-5t51: Structure of the MIND Complex Shows a Regulatory Focus of Yeast K... -

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Basic information

Entry
Database: PDB / ID: 5t51
TitleStructure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly
Components
  • KLLA0E05809p
  • KLLA0F02343p
KeywordsCELL CYCLE / kinetochore / complex / chromosome / segregation / MIND / Mis12
Function / homology
Function and homology information


MIS12/MIND type complex / chromosome segregation / kinetochore / mitotic cell cycle / cell division / nucleus
Similarity search - Function
Kinetochore-associated protein Nnf1 / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein
Similarity search - Domain/homology
KLLA0F02343p / Kinetochore-associated protein
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2007 Å
AuthorsDimitrova, Y. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Grant GM62850 United States
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 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 2.0Nov 20, 2019Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1Mar 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

Downloads & links

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Assembly

Deposited unit
A: KLLA0F02343p
B: KLLA0E05809p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0143
Polymers25,9182
Non-polymers961
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-55 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.630, 82.630, 62.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11B-1133-

HOH

DetailsDimer confirmed by gel filtration

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Components

#1: Protein KLLA0F02343p


Mass: 13816.932 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_F02343g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CLK3
#2: Protein KLLA0E05809p


Mass: 12100.684 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M cacodylate, pH 6.5, 2.0 M ammonium sulfate, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→35.78 Å / Num. obs: 12402 / % possible obs: 97 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.119 / Net I/σ(I): 9
Reflection shellResolution: 2.2007→2.28 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2007→35.78 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 25.59
RfactorNum. reflection% reflection
Rfree0.2531 1200 9.96 %
Rwork0.2077 --
obs0.2123 12051 97.02 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 2.2007→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 5 82 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031545
X-RAY DIFFRACTIONf_angle_d0.4432082
X-RAY DIFFRACTIONf_dihedral_angle_d10.953958
X-RAY DIFFRACTIONf_chiral_restr0.035238
X-RAY DIFFRACTIONf_plane_restr0.002266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2007-2.28880.37391280.29641135X-RAY DIFFRACTION91
2.2888-2.3930.29421220.25931140X-RAY DIFFRACTION94
2.393-2.51910.28391320.23951188X-RAY DIFFRACTION96
2.5191-2.67690.28441330.24211211X-RAY DIFFRACTION97
2.6769-2.88350.30881370.21911210X-RAY DIFFRACTION98
2.8835-3.17350.2571350.20891216X-RAY DIFFRACTION99
3.1735-3.63240.30691280.19271240X-RAY DIFFRACTION99
3.6324-4.57490.17931410.16771250X-RAY DIFFRACTION100
4.5749-35.78460.21881440.19271261X-RAY DIFFRACTION99

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