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Yorodumi- PDB-3hgt: Structural and functional studies of the yeast class II Hda1 HDAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hgt | ||||||
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Title | Structural and functional studies of the yeast class II Hda1 HDAC complex | ||||||
Components | HDA1 complex subunit 3 | ||||||
Keywords | TRANSCRIPTION / RecA-like domain / SWI2/SNF2 helical domain / Chromatin regulator / Coiled coil / Nucleus / Repressor / Transcription regulation | ||||||
Function / homology | Function and homology information HDA1 complex / regulatory ncRNA-mediated gene silencing / chromosome segregation / chromatin remodeling / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lee, J.H. / Maskos, K. / Huber, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural and Functional Studies of the Yeast Class II Hda1 Histone Deacetylase Complex. Authors: Lee, J.H. / Maskos, K. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hgt.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hgt.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hgt_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 3hgt_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | 3hgt_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 3hgt_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/3hgt ftp://data.pdbj.org/pub/pdb/validation_reports/hg/3hgt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 37762.480 Da / Num. of mol.: 2 / Fragment: UNP residues 6-333 / Mutation: K168A, Q169A, K170A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HDA3, PLO1, YPR179C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06623 #2: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0007 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0007 Å / Relative weight: 1 |
Reflection twin | Operator: L,-K,H / Fraction: 0.296 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 33474 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.043 |
Reflection shell | Resolution: 2.2→2.34 Å / Rsym value: 0.11 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.983 Å / σ(F): 1.52 / Phase error: 32.33 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.784 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.983 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 98 %
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