+Open data
-Basic information
Entry | Database: PDB / ID: 1fvi | ||||||
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Title | CRYSTAL STRUCTURE OF CHLORELLA VIRUS DNA LIGASE-ADENYLATE | ||||||
Components | CHLORELLA VIRUS DNA LIGASE-ADENYLATE | ||||||
Keywords | LIGASE / adenylated DNA ligase | ||||||
Function / homology | Function and homology information DNA ligation involved in DNA repair / DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding Similarity search - Function | ||||||
Biological species | Chlorella virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Odell, M. / Sriskanda, V. / Shuman, S. / Nikolov, D.B. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Authors: Odell, M. / Sriskanda, V. / Shuman, S. / Nikolov, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fvi.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fvi.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fvi ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fvi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34124.195 Da / Num. of mol.: 1 / Mutation: D29A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorella virus / Genus: Chlorovirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O41026, UniProt: A7RCB1*PLUS, Ligases; Forming phosphoric-ester bonds |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-AMP / |
#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: 2.1 Å3/Da / Density % sol: 41.39 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 98.6 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.045 |
-Processing
Software |
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Refinement | Resolution: 2→6 Å / σ(F): 1.5 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / σ(F): 1.5 / Rfactor obs: 0.185 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.19 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |