+Open data
-Basic information
Entry | Database: PDB / ID: 3ezp | ||||||
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Title | Crystal Structure Analysis of human HDAC8 D101N variant | ||||||
Components | Histone deacetylase 8 | ||||||
Keywords | HYDROLASE / HDAC / metalloenzyme / arginase fold / HDAC8 / histone deacetylase 8 / hydroxamate inhibitor / mutant / Chromatin regulator / Nucleus / Repressor / Transcription / Transcription regulation | ||||||
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: 2.65 Å | ||||||
Authors | Dowling, D.P. / Gantt, S.L. / Gattis, S.G. / Fierke, C.A. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Authors: Dowling, D.P. / Gantt, S.L. / Gattis, S.G. / Fierke, C.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 | 3ezp.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ezp.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 3ezp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ezp_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3ezp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ezp_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 3ezp_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/3ezp ftp://data.pdbj.org/pub/pdb/validation_reports/ez/3ezp | HTTPS FTP |
-Related structure data
Related structure data | 3ew8C 3ewfC 3eztC 3f06C 3f07C 3f0rC 1t67S 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, 2 molecules AB
#1: Protein | Mass: 43173.957 Da / Num. of mol.: 2 / Mutation: D101N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDA07, HDAC8, HDACL1 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase |
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-Non-polymers , 5 types, 61 molecules
#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | #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: 2.6 Å3/Da / Density % sol: 52.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: Final drop concentrations of 25 mM Tris, 2.5% glycerol, 75 mM KCl, 1-5% PEG MME 35,000, 50 mM MES, 1 mM tri(2-carboxyethyl)phosphine (TCEP), 0.03 mM gly-gly-gly, pH 5.8, VAPOR DIFFUSION, ...Details: Final drop concentrations of 25 mM Tris, 2.5% glycerol, 75 mM KCl, 1-5% PEG MME 35,000, 50 mM MES, 1 mM tri(2-carboxyethyl)phosphine (TCEP), 0.03 mM gly-gly-gly, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2008 |
Radiation | Monochromator: MD2 micro-diffractometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 25531 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 64.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.9 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1T67 Resolution: 2.65→47.23 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 80974.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.35 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→47.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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