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Yorodumi- PDB-2zxp: Crystal structure of RecJ in complex with Mn2+ from Thermus therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zxp | ||||||
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Title | Crystal structure of RecJ in complex with Mn2+ from Thermus thermophilus HB8 | ||||||
Components | Single-stranded DNA specific exonuclease RecJ | ||||||
Keywords | HYDROLASE / nuclease / single-stranded DNA / DNA repair / Exonuclease | ||||||
Function / homology | Function and homology information exonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wakamatsu, T. / Kitamura, Y. / Nakagawa, N. / Masui, R. / Kuramitsu, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure of RecJ exonuclease defines its specificity for single-stranded DNA Authors: Wakamatsu, T. / Kitamura, Y. / Kotera, Y. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zxp.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zxp.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zxp ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zxp | HTTPS FTP |
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-Related structure data
Related structure data | 2zxoSC 2zxrC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 72960.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: recj, TTHA1167 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS References: UniProt: Q5SJ47, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05M ADA, 6% PEG4000, 1% 2-propanol. The crystal was soaked in cryoprotecting solution containg 20% glycerol and 10mM manganese sulfate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.000000, 1.700000 | |||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 1, 2008 | |||||||||
Radiation | Monochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. all: 40110 / Num. obs: 40110 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 50.6 | |||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 9 / Num. unique all: 538276 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENATRY 2ZXO Resolution: 2.3→41.56 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→41.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012
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