+Open data
-Basic information
Entry | Database: PDB / ID: 6jus | ||||||
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Title | MsDpo4-DNA complex 6 | ||||||
Components |
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Keywords | REPLICATION/DNA / DNA polymerase / REPLICATION / REPLICATION-DNA complex | ||||||
Function / homology | Function and homology information SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nair, D.T. / Johnson, M.K. | ||||||
Funding support | India, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: A polar filter in DNA polymerases prevents ribonucleotide incorporation. Authors: Johnson, M.K. / Kottur, J. / Nair, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jus.cif.gz | 332.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jus.ent.gz | 264.9 KB | Display | PDB format |
PDBx/mmJSON format | 6jus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/6jus ftp://data.pdbj.org/pub/pdb/validation_reports/ju/6jus | HTTPS FTP |
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-Related structure data
Related structure data | 6julSC 6jumC 6junC 6juoC 6jupC 6juqC 6jurC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38535.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: dinB, MSMEG_1014, MSMEG_2294 / Variant: ATCC 700084 / mc(2)155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QR77, DNA-directed DNA polymerase #2: DNA chain | Mass: 5508.553 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA template / Source: (synth.) Mycobacterium smegmatis (bacteria) #3: Chemical | #4: Chemical | ChemComp-MN / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.27 Å3/Da / Density % sol: 45.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 2KMME 12%, Bis Tris Propane pH 6.0, NaCl 0.2 mM PH range: 6 / Temp details: 295 K |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44.6 Å / Num. obs: 31909 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.042 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.552 / Num. unique obs: 4401 / Rpim(I) all: 0.268 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JUL Resolution: 2.5→44.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 24.074 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.587 / ESU R Free: 0.296
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.115 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→44.6 Å
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Refine LS restraints |
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