[English] 日本語
Yorodumi- PDB-2xo7: Crystal structure of a dA:O-allylhydroxylamine-dC basepair in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xo7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a dA:O-allylhydroxylamine-dC basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus | |||||||||
Components |
| |||||||||
Keywords | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / EPIGENETICS / PYROSEQUENCING | |||||||||
Function / homology | Function and homology information 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 | GEOBACILLUS STEAROTHERMOPHILUS (bacteria) SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Muenzel, M. / Lercher, L. / Mueller, M. / Carell, T. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2010 Title: Chemical Discrimination between Dc and 5Medc Via Their Hydroxylamine Adducts Authors: Muenzel, M. / Lercher, L. / Mueller, M. / Carell, T. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xo7.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xo7.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/2xo7 ftp://data.pdbj.org/pub/pdb/validation_reports/xo/2xo7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1u45S 2xo9 2xoh 2xoj S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 66219.914 Da / Num. of mol.: 1 / Fragment: RESIDUES 297-876 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Strain: DSM 22 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: C3IXT2, UniProt: E1C9K5*PLUS, DNA-directed DNA polymerase | ||||
---|---|---|---|---|---|
#2: DNA chain | Mass: 3021.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) | ||||
#3: DNA chain | Mass: 3422.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) | ||||
#4: Chemical | ChemComp-SO4 / #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. ...THE ENTRY ABOVE IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM IDENTITY. ONLY T550 IS S IN OUR SEQUENCE.THE CRYSTALLIS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 66.3 % / Description: NONE |
---|---|
Crystal grow | pH: 5.8 Details: 50-55% (NH4)2SO4 3-3.5% MPD 100MM MES, PH 5.8 10MG/ML PROTEIN/DNA 1:3 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→43.74 Å / Num. obs: 20704 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U45 Resolution: 2.85→43.74 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.727 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 33.17 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→43.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|