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- PDB-3t79: Ndc10: a platform for inner kinetochore assembly in budding yeast -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t79 | ||||||
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Title | Ndc10: a platform for inner kinetochore assembly in budding yeast | ||||||
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![]() | DNA BINDING PROTEIN/DNA / DNA recombinase / DNA binding / DNA / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, U.S. / Harrison, S.C. | ||||||
![]() | ![]() Title: Ndc10 is a platform for inner kinetochore assembly in budding yeast. Authors: Cho, U.S. / Harrison, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 361.1 KB | Display | ![]() |
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PDB format | ![]() | 298.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.2 KB | Display | ![]() |
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Full document | ![]() | 555 KB | Display | |
Data in XML | ![]() | 41.3 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sqiSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 4581.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized DNA |
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#2: DNA chain | Mass: 4590.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized DNA |
#3: DNA chain | Mass: 4276.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized DNA |
#4: DNA chain | Mass: 4599.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized DNA |
#5: Protein | Mass: 46610.270 Da / Num. of mol.: 2 / Fragment: DNA binding domain (residues 1-402) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0E03807g / Plasmid: PET3A / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 10,000, 0.1 M Tris-HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010 / Details: MIRRORS |
Radiation | Monochromator: CHOZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. all: 13976 / Num. obs: 13821 / % possible obs: 99 % / Observed criterion σ(I): 22.4 / Redundancy: 3.4 % / Biso Wilson estimate: 67.92 Å2 / Rmerge(I) obs: 0.223 / Net I/σ(I): 1.4 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1374 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SQI Resolution: 3.6113→43.645 Å / SU ML: 0.98 / σ(F): 1.34 / Phase error: 36.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.934 Å2 / ksol: 0.288 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.63 Å2
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Refinement step | Cycle: LAST / Resolution: 3.6113→43.645 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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