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- PDB-4wbq: Crystal structure of the exonuclease domain of QIP (QDE-2 interac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wbq | ||||||
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Title | Crystal structure of the exonuclease domain of QIP (QDE-2 interacting protein) solved by native-SAD phasing. | ||||||
![]() | QDE-2-interacting protein | ||||||
![]() | RNA BINDING PROTEIN | ||||||
Function / homology | Gfd2/YDR514C-like / nucleic acid binding / Ribonuclease H superfamily / Ribonuclease H-like superfamily / metal ion binding / QDE-2-interacting protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boland, A. / Weinert, T. / Weichenrieder, O. / Wang, M. | ||||||
![]() | ![]() Title: Fast native-SAD phasing for routine macromolecular structure determination. Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86 KB | Display | ![]() |
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PDB format | ![]() | 62.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.9 KB | Display | ![]() |
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Full document | ![]() | 433.7 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pgoC ![]() 4piiC ![]() 4r8tC ![]() 4r8uC ![]() 4tn8C ![]() 4tnoC ![]() 4wabC ![]() 4wauC ![]() 4wbxC 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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Unit cell |
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Components
#1: Protein | Mass: 26794.941 Da / Num. of mol.: 2 / Fragment: UNP residues 326-565 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M CaCl2, 0.1M Hepes buffer, pH7, 20% PEG6000 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.0664 Å / Relative weight: 1 |
Reflection | Resolution: 2.693→43 Å / Num. obs: 20707 / % possible obs: 99.9 % / Redundancy: 154 % / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 16.94 / Num. unique all: 2661 / % possible all: 86.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.693→42.963 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: chain 'B' and resid ' 519 ' and name ' SD ' and altloc ' ' |