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Yorodumi- PDB-5fsx: Crystal structure of Trypanosoma brucei macrodomain in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fsx | |||||||||
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Title | Crystal structure of Trypanosoma brucei macrodomain in complex with ADP | |||||||||
Components | MACRODOMAIN | |||||||||
Keywords | HYDROLASE / MACRODOMAIN / ADP-RIBOSE BINDING | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | TRYPANOSOMA BRUCEI (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Haikarainen, T. / Lehtio, L. | |||||||||
Citation | Journal: Sci.Rep. / Year: 2016 Title: Proximal Adp-Ribose Hydrolysis in Trypanosomatids is Catalyzed by a Macrodomain. Authors: Haikarainen, T. / Lehtio, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fsx.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fsx.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fsx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5fsx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5fsx_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 5fsx_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/5fsx ftp://data.pdbj.org/pub/pdb/validation_reports/fs/5fsx | HTTPS FTP |
-Related structure data
Related structure data | 5fsuSC 5fsvC 5fsyC 5fszC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29175.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9ZP98 #2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 47 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.1 M MIB (MALONIC ACID, IMIDAZOLE, BORIC ACID) PH 8.0, 25 % W/V PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2015 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 34730 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 39.67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FSU Resolution: 2→19.433 Å / SU ML: 0.31 / σ(F): 1.53 / Phase error: 35.84 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED TO RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.433 Å
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Refine LS restraints |
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LS refinement shell |
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