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- PDB-4bz8: Crystal structure of Schistosoma mansoni HDAC8 complexed with J1038 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bz8 | ||||||
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Title | Crystal structure of Schistosoma mansoni HDAC8 complexed with J1038 | ||||||
![]() | HISTONE DEACETYLASE 8 | ||||||
![]() | HYDROLASE / PLATYHELMINTHS / HDAC8 / INHIBITOR | ||||||
Function / homology | ![]() histone deacetylase / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marek, M. / Romier, C. | ||||||
![]() | ![]() Title: Structural Basis for the Inhibition of Histone Deacetylase 8 (Hdac8), a Key Epigenetic Player in the Blood Fluke Schistosoma Mansoni. Authors: Marek, M. / Kannan, S. / Hauser, A. / Moraes Mourao, M. / Caby, S. / Cura, V. / Stolfa, D.A. / Schmidtkunz, K. / Lancelot, J. / Andrade, L. / Renaud, J. / Oliveira, G. / Sippl, W. / Jung, M. ...Authors: Marek, M. / Kannan, S. / Hauser, A. / Moraes Mourao, M. / Caby, S. / Cura, V. / Stolfa, D.A. / Schmidtkunz, K. / Lancelot, J. / Andrade, L. / Renaud, J. / Oliveira, G. / Sippl, W. / Jung, M. / Cavarelli, J. / Pierce, R.J. / Romier, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 651.6 KB | Display | ![]() |
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PDB format | ![]() | 540.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.7 KB | Display | ![]() |
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Full document | ![]() | 487.1 KB | Display | |
Data in XML | ![]() | 59.9 KB | Display | |
Data in CIF | ![]() | 84 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bz5C ![]() 4bz6C ![]() 4bz7C ![]() 4bz9C ![]() 1t67S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50444.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-J38 / ( #5: Water | ChemComp-HOH / | Sequence details | THE GSLVPR MOTIF AT THE END OF THE SEQUENCE CORRESPONDS TO A BAMHI CLONING SITE (GS) FOLLOWED BY A ...THE GSLVPR MOTIF AT THE END OF THE SEQUENCE CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.5 Å3/Da / Density % sol: 19 % / Description: NONE |
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Crystal grow | Details: 0.2 M NA,K L-TARTRATE, 21% (W/V) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 84242 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 26.35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.9 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1T67 Resolution: 2.21→32.36 Å / Cor.coef. Fo:Fc: 0.9274 / Cor.coef. Fo:Fc free: 0.8947 / SU R Cruickshank DPI: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.255 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.201
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Displacement parameters | Biso mean: 26.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.262 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→32.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.27 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 63.0938 Å / Origin y: 26.6385 Å / Origin z: 55.5001 Å
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Refinement TLS group | Selection details: ALL |