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Yorodumi- PDB-4pii: Crystal structure of hypothetical protein PF0907 from pyrococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pii | ||||||
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Title | Crystal structure of hypothetical protein PF0907 from pyrococcus furiosus solved by sulfur SAD using Swiss light source data | ||||||
Components | N-glycosylase/DNA lyase | ||||||
Keywords | UNKNOWN FUNCTION / SULFUR SAD / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / STRUCTURAL GENOMICS / SECSG | ||||||
Function / homology | Function and homology information oxidized base lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å | ||||||
Authors | Weinert, T. / Waltersperger, S. / Olieric, V. / Panepucci, E. / Chen, L. / Rose, J.P. / Wang, M. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: Nat.Methods / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pii.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pii.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pii_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 4pii_full_validation.pdf.gz | 444.7 KB | Display | |
Data in XML | 4pii_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4pii_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/4pii ftp://data.pdbj.org/pub/pdb/validation_reports/pi/4pii | HTTPS FTP |
-Related structure data
Related structure data | 4pgoC 4r8tC 4r8uC 4tn8C 4tnoC 4wabC 4wauC 4wbqC 4wbxC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29298.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0904 / Production host: Escherichia coli (E. coli) References: UniProt: Q8U2D5, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase | ||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-IMD / | #4: 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: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 7.3 Details: 0.1 M HEPES buffer containing 3.5M NaCl at pH 7.3. MODIFIED MICROBATCH, TEMPERATURE 291K PH range: 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.066 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.066 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→50 Å / Num. obs: 23632 / % possible obs: 90.4 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 40.45 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.17→49.215 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.28 / Phase error: 25.55 / Stereochemistry target values: MLHL
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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: 2.17→49.215 Å
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Refine LS restraints |
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LS refinement shell |
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