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Yorodumi- PDB-6w9o: Crystal structure of an OTU deubiquitinase from Wolbachia pipient... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w9o | |||||||||
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Title | Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel | |||||||||
Components | OTU domain-containing protein wMelOTU | |||||||||
Keywords | HYDROLASE / Deubiquitinase / Bacterial effector | |||||||||
Function / homology | OTU domain / OTU domain profile. / ACETATE ION / OTU domain-containing protein Function and homology information | |||||||||
Biological species | Wolbachia pipientis wMel (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å | |||||||||
Authors | Schubert, A.F. / Pruneda, J.N. / Komander, D. | |||||||||
Funding support | United Kingdom, European Union, 2items
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Citation | Journal: Embo J. / Year: 2020 Title: Identification and characterization of diverse OTU deubiquitinases in bacteria. Authors: Schubert, A.F. / Nguyen, J.V. / Franklin, T.G. / Geurink, P.P. / Roberts, C.G. / Sanderson, D.J. / Miller, L.N. / Ovaa, H. / Hofmann, K. / Pruneda, J.N. / Komander, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w9o.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w9o.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 6w9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w9o_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 6w9o_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 6w9o_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 6w9o_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/6w9o ftp://data.pdbj.org/pub/pdb/validation_reports/w9/6w9o | HTTPS FTP |
-Related structure data
Related structure data | 6w9rC 6w9sC 3c0rS 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: 24488.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wolbachia pipientis wMel (bacteria) / Gene: WD_0443 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73HU7 |
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#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 32% PEG 4K, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.47→33 Å / Num. obs: 33057 / % possible obs: 99.7 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.061 / Net I/σ(I): 15.4 / Num. measured all: 141445 / Scaling rejects: 13 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C0R Resolution: 1.47→33 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.48 Å2 / Biso mean: 27.0821 Å2 / Biso min: 10.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.47→33 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: -5.6051 Å / Origin y: -11.0613 Å / Origin z: 19.9715 Å
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Refinement TLS group |
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