+Open data
-Basic information
Entry | Database: PDB / ID: 7kdf | ||||||
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Title | Structure of Stu2 Bound to dwarf Ndc80c | ||||||
Components |
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Keywords | CELL CYCLE / Stu2 / tension sensing / Ndc80 / kinetochore | ||||||
Function / homology | Function and homology information repair of mitotic kinetochore microtubule attachment defect / centromere clustering / microtubule plus end polymerase / kinetochore => GO:0000776 / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / establishment or maintenance of microtubule cytoskeleton polarity / meiotic chromosome segregation ...repair of mitotic kinetochore microtubule attachment defect / centromere clustering / microtubule plus end polymerase / kinetochore => GO:0000776 / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / establishment or maintenance of microtubule cytoskeleton polarity / meiotic chromosome segregation / microtubule plus-end / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / spindle pole body / protein localization to kinetochore / microtubule polymerization / mitotic spindle organization / chromosome segregation / spindle microtubule / kinetochore / spindle pole / cell cortex / microtubule binding / cell cycle / cell division / protein-containing complex binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Zahm, J.A. / Stewart, M.G. / Miller, M.P. / Harrison, S.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2021 Title: Structural basis of Stu2 recruitment to yeast kinetochores. Authors: Zahm, J.A. / Stewart, M.G. / Carrier, J.S. / Harrison, S.C. / Miller, M.P. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kdf.cif.gz | 376.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kdf.ent.gz | 257.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kdf_validation.pdf.gz | 477.6 KB | Display | wwPDB validaton report |
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Full document | 7kdf_full_validation.pdf.gz | 487.7 KB | Display | |
Data in XML | 7kdf_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 7kdf_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/7kdf ftp://data.pdbj.org/pub/pdb/validation_reports/kd/7kdf | HTTPS FTP |
-Related structure data
Related structure data | 5tcsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 33041.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NDC80, GI526_G0001489 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6A5Q2M2, UniProt: P40460*PLUS |
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#2: Protein | Mass: 25040.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NUF2, GI526_G0005257 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6A5Q3C2, UniProt: P33895*PLUS |
#3: Protein | Mass: 11881.458 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q04477*PLUS |
#4: Protein | Mass: 12822.623 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPC25, GI526_G0001792 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6A5PX14, UniProt: P40014*PLUS |
-Protein/peptide , 1 types, 1 molecules E
#5: Protein/peptide | Mass: 3812.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTU3, UniProt: P46675*PLUS |
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-Non-polymers , 2 types, 101 molecules
#6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.94 Å3/Da / Density % sol: 75.08 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 1.3 M Ammonium Sulfate 0.1 M Hepes pH 7.3 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→44.06 Å / Num. obs: 52106 / % possible obs: 99.03 % / Redundancy: 13.4 % / Biso Wilson estimate: 63.7 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1071 / Rpim(I) all: 0.03047 / Rrim(I) all: 0.1114 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.72→2.817 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.9043 / Num. unique obs: 62919 / CC1/2: 0.829 / CC star: 0.952 / Rpim(I) all: 0.03047 / Rrim(I) all: 0.9395 / % possible all: 91.15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TCS Resolution: 2.72→42.72 Å / SU ML: 0.3439 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.9868 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→42.72 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -22.7267285986 Å / Origin y: -43.5708296011 Å / Origin z: -24.3484578945 Å
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Refinement TLS group | Selection details: all |