+Open data
-Basic information
Entry | Database: PDB / ID: 1iqr | ||||||
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Title | Crystal structure of DNA photolyase from Thermus thermophilus | ||||||
Components | photolyase | ||||||
Keywords | LYASE / DNA repair / Cyclobutane pyrimidine dimer (CPD) / FAD / Photoreactivating Enzyme / DNA-binding / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA repair / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å | ||||||
Authors | Komori, H. / Masui, R. / Kuramitsu, S. / Yokoyama, S. / Shibata, T. / Inoue, Y. / Miki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism. Authors: Komori, H. / Masui, R. / Kuramitsu, S. / Yokoyama, S. / Shibata, T. / Inoue, Y. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iqr.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iqr.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 1iqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iqr_validation.pdf.gz | 476.7 KB | Display | wwPDB validaton report |
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Full document | 1iqr_full_validation.pdf.gz | 484.3 KB | Display | |
Data in XML | 1iqr_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1iqr_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iqr ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iqr | HTTPS FTP |
-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: 47973.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) References: UniProt: P61497, deoxyribodipyrimidine photo-lyase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-FAD / |
#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: 2.73 Å3/Da / Density % sol: 54.98 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium acetate, Ammonium phosphate, lithium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 3, 2000 | |||||||||||||||
Radiation | Monochromator: a fix-exit double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→25 Å / Num. all: 31913 / Num. obs: 28567 / % possible obs: 89.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.061 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.277 / % possible all: 74 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 25 Å / Redundancy: 3.8 % | |||||||||||||||
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 74 % / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.1→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.214 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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