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Yorodumi- PDB-5qix: Covalent fragment group deposition -- Crystal Structure of OUTB2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qix | ||||||
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Title | Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103007 | ||||||
Components | Ubiquitin thioesterase OTUB2 | ||||||
Keywords | hydrolase/hydrolase inhibitor / SGC - Diamond I04-1 fragment screening / XChemExplorer / PROTEASE OTUB2 / DEUBIQUITINATING ENZYME OTUB2 / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of double-strand break repair / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.39 Å | ||||||
Authors | Sethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. ...Sethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / London, N. / von Delft, F. | ||||||
Citation | Journal: To Be Published Title: Covalent fragment group deposition Authors: Sethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / London, N. / von Delft, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qix.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qix.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 5qix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5qix_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 5qix_full_validation.pdf.gz | 462 KB | Display | |
Data in XML | 5qix_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 5qix_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/5qix ftp://data.pdbj.org/pub/pdb/validation_reports/qi/5qix | HTTPS FTP |
-Group deposition
ID | G_1002053 (12 entries) |
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Title | Covalent fragment group deposition |
Type | changed state |
Description | human OUTB2 screened against covalent fragments by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 1tffS 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: 26362.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OTUB2, C14orf137, OTB2, OTU2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96DC9, ubiquitinyl hydrolase 1 | ||||
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#2: Chemical | ChemComp-J5V / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | Num. of mol.: 3 / Source method: obtained synthetically #5: 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: 2.37 Å3/Da / Density % sol: 48.15 % / Mosaicity: 0.06 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.39→29.17 Å / Num. obs: 48731 / % possible obs: 98.4 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.047 / Rrim(I) all: 0.088 / Net I/σ(I): 9.1 / Num. measured all: 162790 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
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: FOURIER SYNTHESIS Starting model: 1TFF Resolution: 1.39→29.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.075 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 90.49 Å2 / Biso mean: 14.222 Å2 / Biso min: 4.94 Å2
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Refinement step | Cycle: final / Resolution: 1.39→29.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.39→1.426 Å / Total num. of bins used: 20
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