+Open data
-Basic information
Entry | Database: PDB / ID: 4qa1 | ||||||
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Title | Crystal structure of A188T HDAC8 in complex with M344 | ||||||
Components | Histone deacetylase 8 | ||||||
Keywords | HYDROLASE / metalloenzyme / histone deacetylase / enzyme inhibitor complex / Cornelia de Lange Syndrome / arginase/deacetylase fold | ||||||
Function / homology | Function and homology information histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex ...histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / epigenetic regulation of gene expression / HDACs deacetylate histones / Hsp90 protein binding / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Separation of Sister Chromatids / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Decroos, C. / Bowman, C.B. / Moser, J.-A.S. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders. Authors: Decroos, C. / Bowman, C.M. / Moser, J.A. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qa1.cif.gz | 325.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qa1.ent.gz | 262.2 KB | Display | PDB format |
PDBx/mmJSON format | 4qa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qa1_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4qa1_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4qa1_validation.xml.gz | 63.7 KB | Display | |
Data in CIF | 4qa1_validation.cif.gz | 94.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/4qa1 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/4qa1 | HTTPS FTP |
-Related structure data
Related structure data | 4qa0C 4qa2C 4qa3C 4qa4C 4qa5C 4qa6C 4qa7C 3ewfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43262.016 Da / Num. of mol.: 4 / Mutation: A188T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE3 / References: UniProt: Q9BY41, histone deacetylase |
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-Non-polymers , 5 types, 1241 molecules
#2: Chemical | ChemComp-K / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-B3N / #5: Chemical | ChemComp-GOL / #6: 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: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M (Bis(2-hydroxyethyl)-amino-tris(hydroxymethyl)-methane) (BISTRIS, pH = 6.5), 4 mM tris(2-carboxyethyl)phosphine (TCEP), 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2012 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. all: 126947 / Num. obs: 124361 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 22.66 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.92→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2 / Num. unique all: 12138 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EWF Resolution: 1.92→47.614 Å / SU ML: 0.21 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.5 / Stereochemistry target values: ML
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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: 28.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→47.614 Å
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Refine LS restraints |
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LS refinement shell |
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