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Yorodumi- PDB-6hgz: ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hgz | ||||||
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Title | ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-ribose | ||||||
Components | ADP-ribosylhydrolase like 2 | ||||||
Keywords | HYDROLASE / ADP-ribosylation / ADP-ribose / ADPRHL2 / ADP-ribosylhydrolase like 2 | ||||||
Function / homology | Function and homology information peptidyl-serine ADP-deribosylation / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / negative regulation of necroptotic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / chromosome / mitochondrial matrix / DNA repair / magnesium ion binding / nucleus Similarity search - Function | ||||||
Biological species | Latimeria chalumnae (coelacanth) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 | 6hgz.cif.gz | 283 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hgz.ent.gz | 226.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/6hgz ftp://data.pdbj.org/pub/pdb/validation_reports/hg/6hgz | HTTPS FTP |
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-Related structure data
Related structure data | 6g1pC 6g1qC 6g28C 6g2aC 6hh3C 6hh4C 6hh5C 6hh6C 6hozC 2fozS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 9 - 353 / Label seq-ID: 3 - 347
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-Components
#1: Protein | Mass: 38289.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Latimeria chalumnae (coelacanth) / Gene: ADPRHL2 / Production host: Escherichia coli (E. coli) / References: UniProt: H3BCW1 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: 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: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 200 MM AMMONIUM ACETATE, 21 % PEG4000, 100 MM CITRATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.858→71.953 Å / Num. obs: 36681 / % possible obs: 94.9 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.032 / Rrim(I) all: 0.097 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.858→2.008 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.355 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1834 / CC1/2: 0.597 / Rpim(I) all: 0.494 / Rrim(I) all: 1.447 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FOZ Resolution: 1.86→71.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.362 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.185 / 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: 31.773 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→71.95 Å
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Refine LS restraints |
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