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Yorodumi- PDB-1c3r: CRYSTAL STRUCTURE OF AN HDAC HOMOLOG COMPLEXED WITH TRICHOSTATIN A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c3r | ||||||
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Title | CRYSTAL STRUCTURE OF AN HDAC HOMOLOG COMPLEXED WITH TRICHOSTATIN A | ||||||
Components | HDLP (HISTONE DEACETYLASE-LIKE PROTEIN) | ||||||
Keywords | LYASE / ALPHA/BETA FOLD / HYDROXAMIC ACID / CHARGE-RELAY SYSTEM / PENTA-COORDINATED ZINC | ||||||
Function / homology | Function and homology information acetoin catabolic process / histone deacetylase activity / epigenetic regulation of gene expression / metal ion binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Finnin, M.S. / Donigian, J.R. / Pavletich, N.P. | ||||||
Citation | Journal: Nature / Year: 1999 Title: Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Authors: Finnin, M.S. / Donigian, J.R. / Cohen, A. / Richon, V.M. / Rifkind, R.A. / Marks, P.A. / Breslow, R. / Pavletich, N.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c3r.cif.gz | 168.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3r.ent.gz | 134.6 KB | Display | PDB format |
PDBx/mmJSON format | 1c3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c3r_validation.pdf.gz | 501.8 KB | Display | wwPDB validaton report |
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Full document | 1c3r_full_validation.pdf.gz | 537.5 KB | Display | |
Data in XML | 1c3r_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 1c3r_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3r ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3r | HTTPS FTP |
-Related 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: 42701.645 Da / Num. of mol.: 2 / Mutation: C75S, C77S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PGEX-4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: O67135 #2: Chemical | #3: Chemical | #4: 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: 2.31 Å3/Da / Density % sol: 46.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop / Details: microseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 180427 / % possible obs: 93.8 % / Rmerge(I) obs: 0.071 |
Reflection | *PLUS Num. obs: 50796 / Num. measured all: 180427 |
-Processing
Software |
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Refinement | Resolution: 2→20 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||
Refine LS restraints | *PLUS
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