+Open data
-Basic information
Entry | Database: PDB / ID: 6rar | ||||||
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Title | Pmar-Lig_PreS3-Mn | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA ligase / ATP-dependent / ligase-DNA co-crystal structure / determinants in DNA binding | ||||||
Function / homology | Function and homology information DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Prochlorococcus marinus str. MIT 9302 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.785 Å | ||||||
Authors | Leiros, H.K.S. / Williamson, A. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation. Authors: Williamson, A. / 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 | 6rar.cif.gz | 224 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rar.ent.gz | 173.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rar_validation.pdf.gz | 827.5 KB | Display | wwPDB validaton report |
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Full document | 6rar_full_validation.pdf.gz | 836.1 KB | Display | |
Data in XML | 6rar_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 6rar_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/6rar ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6rar | HTTPS FTP |
-Related structure data
Related structure data | 6rasC 6rauSC 6rceC S: Starting model for refinement C: citing same article (ref.) |
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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
-DNA chain , 3 types, 3 molecules BCD
#1: DNA chain | Mass: 6479.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3035.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3342.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules I
#4: Protein | Mass: 49886.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prochlorococcus marinus str. MIT 9302 (bacteria) Gene: EU96_0746 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A2ACP7 |
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-Non-polymers , 4 types, 401 molecules
#5: Chemical | ChemComp-MN / |
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#6: Chemical | ChemComp-AMP / |
#7: Chemical | ChemComp-SO4 / |
#8: 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: 3.73 Å3/Da / Density % sol: 67.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 17-18% PEG 8K, 100 mM ammonium sulfate, 100 mM Bis-Tris pH 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.991872 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.991872 Å / Relative weight: 1 |
Reflection | Resolution: 1.785→68 Å / Num. obs: 57936 / % possible obs: 88.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.084 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 1.785→1.98 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2897 / CC1/2: 0.604 / Rpim(I) all: 0.425 / % possible all: 59.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6rau Resolution: 1.785→24.291 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.785→24.291 Å
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Refine LS restraints |
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LS refinement shell |
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