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- PDB-2y1j: CRYSTAL STRUCTURE OF A R-DIASTEREOMER ANALOGUE OF THE SPORE PHOTO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y1j | ||||||||||||
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Title | CRYSTAL STRUCTURE OF A R-DIASTEREOMER ANALOGUE OF THE SPORE PHOTOPRODUCT IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS | ||||||||||||
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![]() | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA REPAIR / SPORE PHOTOPRODUCT / PHOTOLESION / UV LESION / 5-THYMINYL-5 / 6-DIHYDROTHYMINE | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Heil, K. / Schneider, S. / Mueller, M. / Kneuttinger, A.C. / Carell, T. | ||||||||||||
![]() | ![]() Title: Crystal Structures and Repair Studies Reveal the Identity and the Base-Pairing Properties of the Uv-Induced Spore Photoproduct DNA Lesion. Authors: Heil, K. / Kneuttinger, A.C. / Schneider, S. / Lischke, U. / 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 | ![]() | 147.3 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 461.9 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y1iC ![]() 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
#1: Protein | Mass: 66201.984 Da / Num. of mol.: 1 / Fragment: RESIDUES 297-876 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 22 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ![]() ![]() References: UniProt: D7D223, UniProt: E1C9K5*PLUS, DNA-directed DNA polymerase | ||||
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#2: DNA chain | Mass: 2973.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) | ||||
#3: DNA chain | Mass: 3038.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE ENTRY ABOVE IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM IDENTITY. ONLY T550 IS S IN OUR SEQUENCE. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.91 % / 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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 47859 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.7 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U45 Resolution: 2.15→46.84 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.18 / 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: 22.394 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→46.84 Å
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Refine LS restraints |
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