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Yorodumi- PDB-1zp7: The structure of Bacillus subtilis RecU Holliday junction resolva... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zp7 | ||||||
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Title | The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence specific cleavage. | ||||||
Components | Recombination protein UGenetic recombination | ||||||
Keywords | DNA BINDING PROTEIN / recombination / DNA-binding protein / resolvase | ||||||
Function / homology | Function and homology information crossover junction endodeoxyribonuclease / chromosome segregation / endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å | ||||||
Authors | McGregor, N. / Ayora, S. / Sedelnikova, S. / Carrasco, B. / Alonso, J.C. / Thaw, P. / Rafferty, J. | ||||||
Citation | Journal: Structure / Year: 2005 Title: The Structure of Bacillus subtilis RecU Holliday Junction Resolvase and Its Role in Substrate Selection and Sequence-Specific Cleavage. Authors: McGregor, N. / Ayora, S. / Sedelnikova, S. / Carrasco, B. / Alonso, J.C. / Thaw, P. / Rafferty, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zp7.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zp7.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/1zp7 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/1zp7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 23995.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / Strain: pLysS / References: UniProt: P39792 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.78 % |
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 2, 2004 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.25→19.1 Å / Num. obs: 22690 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.25→19.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.712 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.148 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→19.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.4 Å / Total num. of bins used: 20
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