+Open data
-Basic information
Entry | Database: PDB / ID: 6fx7 | ||||||
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Title | Crystal structure of in vitro evolved Af1521 | ||||||
Components | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | ||||||
Keywords | SIGNALING PROTEIN / Macro domain / ADP-ribose binding | ||||||
Function / homology | Function and homology information ADP-ribosylglutamate hydrolase activity / peptidyl-glutamate ADP-deribosylation / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Karlberg, T. / Thorsell, A.G. / Nowak, K. / Hottiger, M.O. / Schuler, H. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins. Authors: Nowak, K. / Rosenthal, F. / Karlberg, T. / Butepage, M. / Thorsell, A.G. / Dreier, B. / Grossmann, J. / Sobek, J. / Imhof, R. / Luscher, B. / Schuler, H. / Pluckthun, A. / Leslie Pedrioli, D.M. / Hottiger, M.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fx7.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fx7.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fx7_validation.pdf.gz | 727.4 KB | Display | wwPDB validaton report |
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Full document | 6fx7_full_validation.pdf.gz | 727.4 KB | Display | |
Data in XML | 6fx7_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 6fx7_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/6fx7 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/6fx7 | HTTPS FTP |
-Related structure data
Related structure data | 2bfqS S: Starting model for refinement |
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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: 23575.941 Da / Num. of mol.: 1 Mutation: K15R, K35E, Y74C, F97L, I103V, S105G, E110G, Y145R, N162D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Gene: AF_1521 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) References: UniProt: O28751, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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#2: Chemical | ChemComp-AR6 / [( |
#3: 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: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25 %w/v PEG3350, 0,2M sodium chloride, 0.1 M bis-tris, 2mM ADP-ribose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→70.02 Å / Num. obs: 17843 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.119 / Rrim(I) all: 0.221 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.82→1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.528 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 841 / CC1/2: 0.53 / Rpim(I) all: 1.796 / Rrim(I) all: 3.116 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BFQ Resolution: 1.82→70.02 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.117
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Displacement parameters | Biso mean: 30.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.82→70.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.93 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: -20.5563 Å / Origin y: -16.8081 Å / Origin z: 6.8698 Å
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Refinement TLS group | Selection details: { A|* } |