+Open data
-Basic information
Entry | Database: PDB / ID: 1p8l | ||||||
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Title | New Crystal Structure of Chlorella Virus DNA Ligase-Adenylate | ||||||
Components | PBCV-1 DNA ligase | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding Similarity search - Function | ||||||
Biological species | Paramecium bursaria Chlorella virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Odell, M. / Malinina, L. / Teplova, M. / Shuman, S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2003 Title: Analysis of the DNA Joining Repertoire of Chlorella Virus DNA ligase and a New Crystal Structure of the Ligase-Adenylate Intermediate Authors: Odell, M. / Malinina, L. / Sriskanda, V. / Teplova, M. / Shuman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p8l.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p8l.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 1p8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p8l_validation.pdf.gz | 711.5 KB | Display | wwPDB validaton report |
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Full document | 1p8l_full_validation.pdf.gz | 722.8 KB | Display | |
Data in XML | 1p8l_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1p8l_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/1p8l ftp://data.pdbj.org/pub/pdb/validation_reports/p8/1p8l | HTTPS FTP |
-Related structure data
Related structure data | 1fviS 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: 35128.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O41026 |
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#2: Chemical | ChemComp-AMP / |
#3: 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: 2.76 Å3/Da / Density % sol: 55.39 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: hanging drop / pH: 7.5 Details: 4-6% PEG 4000, 50 mM HEPES, 50 mM sodium acetate, pH 7.5, hanging drops, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→15 Å / Num. all: 8265 / Num. obs: 8265 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.092 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 95.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FVI Resolution: 2.95→15 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.876 / SU B: 35.01 / SU ML: 0.56 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.237 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.024 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Lowest resolution: 15 Å / Rfactor Rfree: 0.3035 / Rfactor Rwork: 0.263 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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