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- PDB-6hoz: ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hoz | |||||||||
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Title | ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with inosine diphosphate ribose (IDPr) | |||||||||
![]() | ADP-ribosylhydrolase like 2 | |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() peptidyl-serine ADP-deribosylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ariza, A. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.7 KB | Display | ![]() |
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PDB format | ![]() | 232 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6g1pC ![]() 6g1qC ![]() 6g28C ![]() 6g2aC ![]() 6hgzC ![]() 6hh3C ![]() 6hh4C ![]() 6hh5C ![]() 6hh6C ![]() 2fozS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 436 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/R5I.gif)
![](data/chem/img/R7I.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/R5I.gif)
![](data/chem/img/R7I.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / ![]() #6: Chemical | ChemComp-ACT / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.77→96.95 Å / Num. obs: 68856 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.051 / Rrim(I) all: 0.13 / Χ2: 0.96 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.896 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5010 / CC1/2: 0.745 / Rpim(I) all: 0.912 / Rrim(I) all: 2.108 / Χ2: 0.98 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2FOZ Resolution: 1.77→72.1 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 5.435 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.101 / 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: 30.833 Å2
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Refinement step | Cycle: 1 / Resolution: 1.77→72.1 Å
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Refine LS restraints |
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