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Yorodumi- PDB-3ted: Crystal structure of the Chd1 DNA-binding domain in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3ted | ||||||
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Title | Crystal structure of the Chd1 DNA-binding domain in complex with a DNA duplex | ||||||
Components |
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Keywords | DNA binding protein/DNA / PROTEIN-DNA complex / DOUBLE HELIX / DNA DUPLEX / SANT and SLIDE domains / chromatin remodeling / DNA binding / nuclear / DNA binding protein-DNA complex | ||||||
Function / homology | Function and homology information nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / SAGA complex / sister chromatid cohesion ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / SAGA complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sharma, A. / Jenkins, K.R. / Heroux, A. / Bowman, G.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: DNA-binding domain of Chd1 in complex with a DNA duplex Authors: Sharma, A. / Jenkins, K.R. / Heroux, A. / Bowman, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ted.cif.gz | 139.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ted.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ted.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ted_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
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Full document | 3ted_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 3ted_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3ted_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/3ted ftp://data.pdbj.org/pub/pdb/validation_reports/te/3ted | HTTPS FTP |
-Related structure data
Related structure data | 2xb0S 2yz9 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
#1: Protein | Mass: 30505.826 Da / Num. of mol.: 1 Fragment: SANT/SLIDE DNA-binding domain, UNP residues 1006-1274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CHD1, SYGP-ORF4, YER164W / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) References: UniProt: P32657, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#2: DNA chain | Mass: 3621.392 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: artificial AT-rich sequence; synthesized by Integrated DNA Technologies |
#3: DNA chain | Mass: 3701.440 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: artificial AT-rich sequence; synthesized by Integrated DNA Technologies |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 14-18% PEG 400 0.1 M BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 22675 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.2 % / Rsym value: 0.079 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 15 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.768 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2XB0 Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.26 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.726 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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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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