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Open data
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Basic information
Entry | Database: PDB / ID: 6juo | ||||||
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Title | MsDpo4-DNA complex 4 | ||||||
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![]() | REPLICATION/DNA / DNA polymerase / REPLICATION / REPLICATION-DNA complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nair, D.T. / Johnson, M.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A polar filter in DNA polymerases prevents ribonucleotide incorporation. Authors: Johnson, M.K. / Kottur, J. / Nair, D.T. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.3 KB | Display | ![]() |
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PDB format | ![]() | 267.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6julSC ![]() 6jumC ![]() 6junC ![]() 6jupC ![]() 6juqC ![]() 6jurC ![]() 6jusC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38585.828 Da / Num. of mol.: 2 / Mutation: L14Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: dinB, MSMEG_1014, MSMEG_2294 / Variant: ATCC 700084 / mc(2)155 / Production host: ![]() ![]() #2: DNA chain | Mass: 5508.553 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA template / Source: (synth.) ![]() #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 2KMME 12%, 0.2mM NaCl, Bis Tris Propane 6.0 / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.16→70.177 Å / Num. obs: 50583 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.039 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.16→2.28 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 7237 / CC1/2: 0.884 / Rpim(I) all: 0.199 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JUL Resolution: 2.16→70.177 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.927 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.21 / Details: HYDROGENS WERE NOT ADDED
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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: 42.932 Å2
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Refinement step | Cycle: 1 / Resolution: 2.16→70.177 Å
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Refine LS restraints |
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