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Yorodumi- PDB-2xry: X-ray structure of archaeal class II CPD photolyase from Methanos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xry | ||||||
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Title | X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei | ||||||
Components | DEOXYRIBODIPYRIMIDINE PHOTOLYASE | ||||||
Keywords | LYASE / DNA DAMAGE / DNA REPAIR | ||||||
Function / homology | Function and homology information photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | METHANOSARCINA MAZEI (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kiontke, S. / Geisselbrecht, Y. / Pokorny, R. / Carell, T. / Batschauer, A. / Essen, L.O. | ||||||
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 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xry.cif.gz | 221.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xry.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/2xry ftp://data.pdbj.org/pub/pdb/validation_reports/xr/2xry | HTTPS FTP |
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-Related 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 / Fragment: RESIDUES 3-464 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOSARCINA MAZEI (archaea) / Strain: GO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD References: UniProt: Q8PYK9, deoxyribodipyrimidine photo-lyase | ||||||||
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#2: Chemical | ChemComp-FAD / | ||||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | 2 RESIDUES (MET, ILE) DELETED AT THE 6 N-TERMINUS. | |
-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: NONE |
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Crystal grow | Details: 0.5 M LITHIUM SULFATE, 7.5% (W/V) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.88567 |
Detector | Type: ADSC CCD / 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 |
Reflection | Resolution: 1.5→19.94 Å / Num. obs: 95566 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.4 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED STRUCTURAL DATA OF M. BARKERI PHOTOLYASE Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.055 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 189-197 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.396 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→15 Å
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Refine LS restraints |
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