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- PDB-2xy7: Crystal structure of a salicylic aldehyde base in the pre-inserti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xy7 | |||||||||
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Title | Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA polymerase I from Bacillus stearothermophilus | |||||||||
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![]() | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / SYNTHETIC BIOLOGY / METAL BASEPAIR / REPLICATION / SALEN COMPLEX | |||||||||
Function / homology | ![]() double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() SYNTHETIC CONSTRUCT (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kaul, C. / Mueller, M. / Wagner, M. / Schneider, S. / Carell, T. | |||||||||
![]() | ![]() Title: Reversible Bond Formation Enables the Replication and Amplification of a Crosslinking Salen Complex as an Orthogonal Base Pair. Authors: Kaul, C. / Mueller, M. / Wagner, M. / Schneider, S. / Carell, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.3 KB | Display | ![]() |
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PDB format | ![]() | 102.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.5 KB | Display | ![]() |
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Full document | ![]() | 794.7 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xy5C ![]() 2xy6C ![]() 1u45S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3020.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: POLYDESOXYRIBONUCLEOTIDE / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: DNA chain | Mass: 3370.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: POLYDESOXYRIBONUCLEOTIDE / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 66175.898 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 22 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ![]() ![]() |
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#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
-Non-polymers , 2 types, 10 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | THE ENTRY GIVEN IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM IDENTITY. ONLY T550 IS S IN OUR SEQUENCE. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.46 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→46.4 Å / Num. obs: 16829 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3.05→3.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U45 Resolution: 3.05→43.02 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.835 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.531 Å2
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Refinement step | Cycle: LAST / Resolution: 3.05→43.02 Å
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Refine LS restraints |
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