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Yorodumi- PDB-6g1p: Apo form of ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g1p | ||||||
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Title | Apo form of ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae | ||||||
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: 1.55 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 | 6g1p.cif.gz | 300.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g1p.ent.gz | 243.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/6g1p ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g1p | HTTPS FTP |
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-Related structure data
Related structure data | 6g1qC 6g28C 6g2aC 6hgzC 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 600 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / #6: 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: 2.29 Å3/Da / Density % sol: 46.23 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 200 mM ammonium acetate, 21 % (w/v) PEG4000, 100 mM citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→99.88 Å / Num. obs: 102142 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4969 / CC1/2: 0.775 / Rpim(I) all: 0.415 / Rrim(I) all: 0.78 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FOZ Resolution: 1.55→73.21 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.484 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / 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: 22.84 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→73.21 Å
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Refine LS restraints |
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