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Yorodumi- PDB-6gdr: DNA binding with a minimal scaffold: Structure-function analysis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gdr | ||||||
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Title | DNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases | ||||||
Components |
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Keywords | LIGASE / DNA ligases | ||||||
Function / homology | Function and homology information DNA ligase (ATP) activity / DNA recombination / DNA repair / ATP binding Similarity search - Function | ||||||
Biological species | Alteromonas mediterranea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Williamson, A. / Grigic, M. / Leiros, H.K.S. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases. Authors: Williamson, A. / Grgic, M. / Leiros, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gdr.cif.gz | 149.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gdr.ent.gz | 114.3 KB | Display | PDB format |
PDBx/mmJSON format | 6gdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gdr_validation.pdf.gz | 793.3 KB | Display | wwPDB validaton report |
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Full document | 6gdr_full_validation.pdf.gz | 795.7 KB | Display | |
Data in XML | 6gdr_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6gdr_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/6gdr ftp://data.pdbj.org/pub/pdb/validation_reports/gd/6gdr | HTTPS FTP |
-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
-DNA chain , 3 types, 3 molecules BCD
#1: DNA chain | Mass: 6494.194 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: DNA chain | Mass: 3004.981 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Production host: Escherichia coli (E. coli) |
#3: DNA chain | Mass: 3342.212 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Production host: Escherichia coli (E. coli) |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 33017.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Gene: BM525_03130 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J0SCU0 |
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-Non-polymers , 3 types, 72 molecules
#5: Chemical | #6: Chemical | ChemComp-AMP / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 24% PEG 4K, 100 mM Bis-Tris pH 5.5, 12% ethyleneglycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→47.92 Å / Num. obs: 22739 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 39.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.046 / Rrim(I) all: 0.088 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.387 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2184 / CC1/2: 0.493 / Rpim(I) all: 0.0858 / Rrim(I) all: 1.635 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model Resolution: 2.33→24.84 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→24.84 Å
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Refine LS restraints |
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LS refinement shell |
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