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Yorodumi- PDB-2xo6: DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xo6 | ||||||
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Title | DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX / TRANSPOSITION / MOBILE ELEMENT | ||||||
Function / homology | Function and homology information transposase activity / DNA transposition / endonuclease activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hickman, A.B. / James, J.A. / Barabas, O. / Pasternak, C. / Ton-Hoang, B. / Chandler, M. / Sommer, S. / Dyda, F. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: DNA Recognition and the Precleavage State During Single-Stranded DNA Transposition in D. Radiodurans. Authors: Hickman, A.B. / James, J.A. / Barabas, O. / Pasternak, C. / Ton-Hoang, B. / Chandler, M. / Sommer, S. / Dyda, F. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xo6.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xo6.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xo6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/2xo6 ftp://data.pdbj.org/pub/pdb/validation_reports/xo/2xo6 | HTTPS FTP |
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-Related structure data
Related structure data | 2xm3SC 2xmaC 2xqcC 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
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 16119.772 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83028 |
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-DNA chain , 2 types, 4 molecules BECF
#2: DNA chain | Mass: 8252.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 1839.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DRA2 TRANSPOSON INTERNAL SEQUENCE / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-Non-polymers , 4 types, 421 molecules
#4: Chemical | ChemComp-CD / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | TRANSPOSAS | |
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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: 2.68 Å3/Da / Density % sol: 53.9 % / Description: NONE |
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Crystal grow | Temperature: 292 K / pH: 4.8 Details: COMPLEX BUFFER: 35MM TRIS-HCL PH 8.0 0.15M NACL, 10MM MGCL2, 0.5 MM TCEP. PRECIPITATING AGENT: 10MM CDCL2, 0.1M NA-ACETATE PH 4.8, 14% PEG4000. PROTEIN AT 9MG/ML IN COMPLEX BUFFER WAS MIXED ...Details: COMPLEX BUFFER: 35MM TRIS-HCL PH 8.0 0.15M NACL, 10MM MGCL2, 0.5 MM TCEP. PRECIPITATING AGENT: 10MM CDCL2, 0.1M NA-ACETATE PH 4.8, 14% PEG4000. PROTEIN AT 9MG/ML IN COMPLEX BUFFER WAS MIXED WITH LE27 AND T5G. PROTEIN AND DNA OLIGONUCLEOTIDES WERE MIXED IN THE RATIO 1:1.1:1.3. EQUAL VOLUMES OF THIS COMPLEX AND PRECIPITATING AGENT WAS MIXED AT 19 C. CRYOPROTECTION IN 20% V/V GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 2, 2008 / Details: MULTILAYER MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 44818 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.44 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 6.91 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XM3 Resolution: 1.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 Details: AS THE CRYSTALS WERE GROWN IN THE PRESENCE OF BOTH MG2+ AND CD2+, SOME METAL-ION BINDING SITES CONTAINED BOTH AT THE SAME POSITION WITH PARTIAL OCCUPANCIES. THIS WAS OBSERVED IN FO-FC ...Details: AS THE CRYSTALS WERE GROWN IN THE PRESENCE OF BOTH MG2+ AND CD2+, SOME METAL-ION BINDING SITES CONTAINED BOTH AT THE SAME POSITION WITH PARTIAL OCCUPANCIES. THIS WAS OBSERVED IN FO-FC DIFFERENCE MAPS AND ANOMALOUS DIFFERENCE MAPS.
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Solvent computation | Solvent model: FLAT MODE / Bsol: 42.5371 Å2 / ksol: 0.351729 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Xplor file |
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