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- PDB-7f8t: Re-refinement of the 2XRY X-ray structure of archaeal class II CP... -
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Open data
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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 | |||||||||
![]() | Deoxyribodipyrimidine photolyase | |||||||||
![]() | LYASE / Oxidoreductase / redox state / photoreduction / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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 | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226 KB | Display | ![]() |
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PDB format | ![]() | 176.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 885 KB | Display | ![]() |
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Full document | ![]() | 893.7 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() | ||||||||
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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 |