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Yorodumi- PDB-7f8t: Re-refinement of the 2XRY X-ray structure of archaeal class II CP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f8t | |||||||||
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Title | Re-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei | |||||||||
Components | Deoxyribodipyrimidine photolyase | |||||||||
Keywords | LYASE / Oxidoreductase / redox state / photoreduction / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / DNA repair / DNA binding Similarity search - Function | |||||||||
Biological species | Methanosarcina mazei (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Maestre-Reyna, M. / Yang, C.-H. / Huang, W.C. / Nango, E. / Gusti-Ngurah-Putu, E.-P. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Liao, J.-H. ...Maestre-Reyna, M. / Yang, C.-H. / Huang, W.C. / Nango, E. / Gusti-Ngurah-Putu, E.-P. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Liao, J.-H. / Lee, C.-C. / Huang, K.-F. / Chang, Y.-K. / Weng, J.-H. / Sugahara, M. / Owada, S. / Joti, Y. / Tanaka, R. / Tono, K. / Kiontke, S. / Yamamoto, J. / Iwata, S. / Essen, L.-O. / Bessho, Y. / Tsai, M.-D. | |||||||||
Funding support | Taiwan, Japan, 2items
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Citation | Journal: Embo J. / Year: 2011 Title: Crystal Structures of an Archaeal Class II DNA Photolyase and its Complex with Uv-Damaged Duplex DNA. Authors: Kiontke, S. / Geisselbrecht, Y. / Pokorny, R. / Carell, T. / Batschauer, A. / Essen, L.O. | |||||||||
History |
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Remark 0 | This entry 7f8t reflects an alternative modeling of the original structural data R2xrySF determined ...This entry 7f8t reflects an alternative modeling of the original structural data R2xrySF determined by authors of the PDB entry 2XRY: AUTHOR S.KIONTKE,Y.GEISSELBRECHT,R.POKORNY,T.CARELL,A.BATSCHAUER,L.O.ESSEN |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f8t.cif.gz | 226 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f8t.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 7f8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/7f8t ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f8t | HTTPS FTP |
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-Related structure data
Related structure data | 7viwC 7vixC 7viyC 7vizC 7vj0C 7vj1C 7vj2C 7vj3C 7vj4C 7vj5C 7vj6C 7vj7C 7vj8C 7vj9C 7vjaC 7vjbC 7vjcC 7vjeC 7vjgC 7vjhC 7vjiC 7vjjC 7vjkC 2xryS 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: 55123.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F8I5V2 | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-FAD / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.25 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2XRY. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.5 M LITHIUM SULFATE, 7.5% (W/V) PEG 8000 |
-Data collection
Diffraction | Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.88567 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88567 Å / Relative weight: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XRY Resolution: 1.5→19.94 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.13 / Stereochemistry target values: ML
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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: 1.5→19.94 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 18.6387 Å / Origin y: 24.7176 Å / Origin z: 104.7065 Å
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Refinement TLS group | Selection details: all |