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Yorodumi- PDB-2wq7: Structure of the 6-4 photolyase of D. melanogaster in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wq7 | |||||||||
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Title | Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(6-4)C lesion | |||||||||
Components |
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Keywords | LYASE/DNA / LYASE-DNA COMPLEX / DNA REPAIR / DNA LESION / LYASE | |||||||||
Function / homology | Function and homology information deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Glas, A.F. / Kaya, E. / Schneider, S. / Maul, M.J. / Carell, T. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: DNA (6-4) Photolyases Reduce Dewar Isomers for Isomerization Into (6-4) Lesions. Authors: Glas, A.F. / Kaya, E. / Schneider, S. / Heil, K. / Fazio, D. / Maul, M.J. / Carell, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wq7.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wq7.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wq7_validation.pdf.gz | 838.7 KB | Display | wwPDB validaton report |
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Full document | 2wq7_full_validation.pdf.gz | 846.4 KB | Display | |
Data in XML | 2wq7_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 2wq7_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/2wq7 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/2wq7 | HTTPS FTP |
-Related structure data
Related structure data | 2wq6C 3cvuS C: citing same article (ref.) 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: 62910.137 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PDEST007 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-GAMI PLYSS (DE3) References: UniProt: Q8SXK5, deoxyribodipyrimidine photo-lyase |
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#2: DNA chain | Mass: 4651.054 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 4545.948 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-FAD / |
#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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Details: 100MM HEPES PH 7, 13-17% PEG1500 18DGC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.5 Å / Num. obs: 48536 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 26.67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CVU Resolution: 2→40.468 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 19.97 / Stereochemistry target values: ML Details: RESIDUES DT 8 AND DC 9 HAVE FORMED A 6-4 PHOTOPRODUCT BY THE COVALENT BONDING OF ATOM C6 OF TDY TO C4 OF Z.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.351 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40.468 Å
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Refine LS restraints |
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LS refinement shell |
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