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Yorodumi- PDB-4cqf: Crystal structure of Schistosoma mansoni HDAC8 complexed with a m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cqf | ||||||
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Title | Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor | ||||||
Components | HISTONE DEACETYLASE 8 | ||||||
Keywords | HYDROLASE / STRUCTURAL PROTEIN / EUKARYOTES / PLATYHELMINTHS / EPIGENETICS / HISTONE DEACETYLASES / INHIBITION | ||||||
Function / homology | Function and homology information histone deacetylase / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | SCHISTOSOMA MANSONI (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Marek, M. / Romier, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Molecular Basis for the Anti-Parasitic Activity of a Mercaptoacetamide Derivative that Inhibits Histone Deacetylase 8 (Hdac8) from the Human Pathogen Schistosoma Mansoni Authors: Stolfa, D.A. / Marek, M. / Lancelot, J. / Hauser, A.T. / Walter, A. / Leproult, E. / Melesina, J. / Rumpf, T. / Wurtz, J.M. / Cavarelli, J. / Sippl, W. / Pierce, R.J. / Romier, C. / Jung, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cqf.cif.gz | 652.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cqf.ent.gz | 540.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cqf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4cqf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4cqf_validation.xml.gz | 61.2 KB | Display | |
Data in CIF | 4cqf_validation.cif.gz | 83.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/4cqf ftp://data.pdbj.org/pub/pdb/validation_reports/cq/4cqf | HTTPS FTP |
-Related structure data
Related structure data | 4bz6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 50444.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PNEA/TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5H660 |
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-Non-polymers , 6 types, 485 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-9Z8 / #5: Chemical | ChemComp-DMF / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 80076 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 33.74 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.2 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BZ6 Resolution: 2.3→32.89 Å / Cor.coef. Fo:Fc: 0.9306 / Cor.coef. Fo:Fc free: 0.8976 / SU R Cruickshank DPI: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.3 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.221 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN K. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=13636. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN K. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=13636. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=12.
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Displacement parameters | Biso mean: 26.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.298 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→32.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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