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- PDB-2yfv: The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yfv | ||||||
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Title | The heterotrimeric complex of Kluyveromyces lactis Scm3, Cse4 and H4 | ||||||
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![]() | CELL CYCLE / KINETOCHORE / CENTROMERE / HISTONE CHAPERONE / BUDDING YEAST | ||||||
Function / homology | ![]() CENP-A containing nucleosome binding / condensed chromosome, centromeric region => GO:0000779 / protein localization to chromosome, centromeric region / kinetochore assembly / CENP-A containing nucleosome / negative regulation of ubiquitin-dependent protein catabolic process / chromosome segregation / structural constituent of chromatin / G2/M transition of mitotic cell cycle / nucleosome assembly ...CENP-A containing nucleosome binding / condensed chromosome, centromeric region => GO:0000779 / protein localization to chromosome, centromeric region / kinetochore assembly / CENP-A containing nucleosome / negative regulation of ubiquitin-dependent protein catabolic process / chromosome segregation / structural constituent of chromatin / G2/M transition of mitotic cell cycle / nucleosome assembly / histone binding / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, U.S. / Harrison, S.C. | ||||||
![]() | ![]() Title: Recognition of the Centromere-Specific Histone Cse4 by the Chaperone Scm3. 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 | ![]() | 98.3 KB | Display | ![]() |
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PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 444.6 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yfwC ![]() 1eqzS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11692.733 Da / Num. of mol.: 1 / Fragment: RESIDUES 81-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PET3A / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 8456.876 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-98 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PET3A / Production host: ![]() ![]() | ||
#3: Protein | Mass: 7430.433 Da / Num. of mol.: 1 / Fragment: RESIDUES 41-103 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PET3A / Production host: ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 0.1 M SODIUM CITRATE, PH4.5, 6% PEG 4000, AND 0.1 M SODIUM IODIDE |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2010 / Details: MIRRORS |
Radiation | Monochromator: CHOZU HLD8-24 MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 11636 / % possible obs: 94.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.5 / % possible all: 55.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EQZ Resolution: 2.32→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.225 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 126-130 OF CHAIN A ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.054 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→50 Å
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Refine LS restraints |
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