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Yorodumi- PDB-6g28: Human [protein ADP-ribosylargenine] hydrolase ARH1 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g28 | ||||||
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Title | Human [protein ADP-ribosylargenine] hydrolase ARH1 in complex with ADP-ribose | ||||||
Components | [Protein ADP-ribosylarginine] hydrolase | ||||||
Keywords | HYDROLASE / ADP-ribosylation / ADP-ribose / ADPRH / ADP-ribosylhydrolase / ARH1 | ||||||
Function / homology | Function and homology information [protein ADP-ribosylarginine] hydrolase / ADP-ribosylarginine hydrolase activity / protein de-ADP-ribosylation / potassium ion binding / protein modification process / magnesium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å | ||||||
Authors | Ariza, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell Chem Biol / Year: 2018 Title: (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition. Authors: Rack, J.G.M. / Ariza, A. / Drown, B.S. / Henfrey, C. / Bartlett, E. / Shirai, T. / Hergenrother, P.J. / Ahel, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g28.cif.gz | 176.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g28.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 6g28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g28_validation.pdf.gz | 780.4 KB | Display | wwPDB validaton report |
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Full document | 6g28_full_validation.pdf.gz | 782.4 KB | Display | |
Data in XML | 6g28_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 6g28_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/6g28 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/6g28 | HTTPS FTP |
-Related structure data
Related structure data | 6g1pC 6g1qC 6g2aC 6hgzC 6hh3C 6hh4C 6hh5C 6hh6C 6hozC 3hfwS 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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Unit cell |
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-Components
#1: Protein | [ Mass: 40684.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRH, ARH1 / Production host: Escherichia coli (E. coli) References: UniProt: P54922, [protein ADP-ribosylarginine] hydrolase | ||||
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#2: Chemical | ChemComp-AR6 / [( | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM magnesium formate, 20 % (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→66.69 Å / Num. obs: 103868 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.23→1.25 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 4932 / CC1/2: 0.981 / Rpim(I) all: 0.132 / Rrim(I) all: 0.295 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HFW Resolution: 1.23→52.09 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.158 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.97 Å2
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Refinement step | Cycle: 1 / Resolution: 1.23→52.09 Å
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Refine LS restraints |
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