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Open data
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Basic information
Entry | Database: PDB / ID: 1c3s | ||||||
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Title | CRYSTAL STRUCTURE OF AN HDAC HOMOLOG COMPLEXED WITH SAHA | ||||||
![]() | HDLP (HISTONE DEACETYLASE-LIKE PROTEIN) | ||||||
![]() | LYASE / ALPHA/BETA FOLD / HYDROXAMIC ACID / PENTA-COORDINATED ZINC / CHARGE-RELAY SYSTEM | ||||||
Function / homology | ![]() acetoin catabolic process / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Finnin, M.S. / Donigian, J.R. / Pavletich, N.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.2 KB | Display | ![]() |
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PDB format | ![]() | 67.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.1 KB | Display | ![]() |
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Full document | ![]() | 439.1 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.: 1 / Mutation: C75S, C77S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SHH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: TERT-BUTANOL, PEG 1500, POTASSIUM CHLORIDE, BIS-TRIS PROPANE-Cl, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: used to seeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() |
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: 2.5→20 Å / Num. all: 11748 / % possible obs: 90.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.086 |
Reflection | *PLUS Num. obs: 11748 / Num. measured all: 27568 |
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Processing
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Refinement | Resolution: 2.5→20 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. reflection obs: 11113 / σ(F): 1 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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