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Yorodumi- PDB-4d05: Structure and activity of a minimal-type ATP-dependent DNA ligase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d05 | |||||||||
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Title | Structure and activity of a minimal-type ATP-dependent DNA ligase from a psychrotolerant bacterium | |||||||||
Components | ATP-DEPENDENT DNA LIGASE | |||||||||
Keywords | LIGASE | |||||||||
Function / homology | Function and homology information DNA ligase (ATP) activity / DNA recombination / DNA repair / ATP binding Similarity search - Function | |||||||||
Biological species | PSYCHROMONAS SP. SP041 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | |||||||||
Authors | Williamson, A. / Rothweiler, U. / Leiros, H.-K.S. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Enzyme-Adenylate Structure of a Bacterial ATP-Dependent DNA Ligase with a Minimized DNA-Binding Surface Authors: Williamson, A. / Rothweiler, U. / Leiros, H.-K.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d05.cif.gz | 322.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d05.ent.gz | 281.1 KB | Display | PDB format |
PDBx/mmJSON format | 4d05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d05_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4d05_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4d05_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4d05_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/4d05 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/4d05 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 29800.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LINK BETWEEN AMP AND LYS173 / Source: (gene. exp.) PSYCHROMONAS SP. SP041 (bacteria) Description: PSYCHROMONAS SP. STRAIN SP041 (GENBANK ACCESSION NO. ERP003516) Plasmid: PHMGWA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: A0A0A6YVN6*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Sequence details | (GENBANK ACCESSION NO. ERP003516) | |
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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: 2.84 Å3/Da / Density % sol: 56.64 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.75 M AMMONIUM SULFATE, 100 MM HEPES PH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→44 Å / Num. obs: 80785 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 14.48 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.65→24.61 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→24.61 Å
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Refine LS restraints |
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LS refinement shell |
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