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- PDB-2xy6: Crystal structure of a salicylic aldehyde basepair in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xy6 | ||||||
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Title | Crystal structure of a salicylic aldehyde basepair in complex with 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 | ![]() | 146.4 KB | Display | ![]() |
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PDB format | ![]() | 108.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.6 KB | Display | ![]() |
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Full document | ![]() | 488.3 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xy5C ![]() 2xy7C ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 66321.016 Da / Num. of mol.: 1 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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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 2951.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: DNA chain | Mass: 3121.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 4 types, 162 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-MRD / ( | #7: Water | ChemComp-HOH / | |
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-Details
Sequence 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: 3.28 Å3/Da / Density % sol: 62.54 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3785 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 39334 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U45 Resolution: 2.3→45.28 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.271 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.221 / 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: 23.277 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.28 Å
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Refine LS restraints |
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