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Yorodumi- PDB-7p2v: Crystal structure of Schistosoma mansoni HDAC8 in complex with a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p2v | ||||||
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Title | Crystal structure of Schistosoma mansoni HDAC8 in complex with a 4-chlorophenyl-spiroindoline capped hydroxamate-based inhibitor, bound to a novel site | ||||||
Components | Histone deacetylase 8 | ||||||
Keywords | HYDROLASE / SmHDAC8 / novel binding-site / HDACi / histone-deacetilase inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Saccoccia, F. / Gemma, S. / Campiani, G. / Ruberti, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors. Authors: Saccoccia, F. / Pozzetti, L. / Gimmelli, R. / Butini, S. / Guidi, A. / Papoff, G. / Giannaccari, M. / Brogi, S. / Scognamiglio, V. / Gemma, S. / Ruberti, G. / Campiani, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p2v.cif.gz | 175.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p2v.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 7p2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/7p2v ftp://data.pdbj.org/pub/pdb/validation_reports/p2/7p2v | HTTPS FTP |
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-Related structure data
Related structure data | 7p2sC 7p2tC 7p2uC 7pozC 4bz5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49834.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: HDAC8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5H660 |
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-Non-polymers , 6 types, 104 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-TLA / | #5: Chemical | ChemComp-4XI / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.36 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 20-22% PEG 3350, 200mM sodium/potassium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2020 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si111 with LN2 closed loop cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→39.14 Å / Num. obs: 23731 / % possible obs: 100 % / Redundancy: 24.9 % / Biso Wilson estimate: 37.57 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.449 / Rpim(I) all: 0.091 / Rrim(I) all: 0.458 / Net I/σ(I): 5.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4bz5 Resolution: 2.25→39.14 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0.53 / Phase error: 28.4 / Stereochemistry target values: ML Details: Refinement has been run by including XYZ refinement both in reciprocal and real-space, group and individual B-factors, TLS, occupancies, and by optimizing X-ray to stereochemistry and ADP weights.
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.26 Å2 / Biso mean: 45.015 Å2 / Biso min: 25.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→39.14 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -9.0857 Å / Origin y: 22.8215 Å / Origin z: 17.1362 Å
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Refinement TLS group |
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