+Open data
-Basic information
Entry | Database: PDB / ID: 2xm3 | ||||||
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Title | Deinococcus radiodurans ISDra2 Transposase Left end DNA complex | ||||||
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 / SIRAS / Resolution: 2.3 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xm3.cif.gz | 277.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xm3.ent.gz | 217.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xm3_validation.pdf.gz | 553.2 KB | Display | wwPDB validaton report |
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Full document | 2xm3_full_validation.pdf.gz | 585.2 KB | Display | |
Data in XML | 2xm3_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 2xm3_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/2xm3 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/2xm3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 16135.772 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: ISDRA2 INSERTION SEQUENCE 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, 12 molecules GIKMOQHJLNPR
#2: DNA chain | Mass: 8252.322 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 1510.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: ISDRA2 INSERTION SEQUENCE LEFT END FLANK / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-Non-polymers , 4 types, 526 molecules
#4: Chemical | ChemComp-ACT / | ||||
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#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Details
Sequence details | TRANSPOSON |
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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: 2.99 Å3/Da / Density % sol: 58.96 % / Description: NONE |
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Crystal grow | Temperature: 292 K / pH: 4.6 Details: COMPLEX BUFFER: 25 MM TRIS/HCL PH 8.0, 0.15M NACL PRECIPITATING AGENT: 17% PEG 6000, 50 MM NAACETATE PH 4.6 10MG/ML COMPLEX MIXED WITH EQUAL AMOUNT OF PRECIPITATING AGENT AT 19 C, ...Details: COMPLEX BUFFER: 25 MM TRIS/HCL PH 8.0, 0.15M NACL PRECIPITATING AGENT: 17% PEG 6000, 50 MM NAACETATE PH 4.6 10MG/ML COMPLEX MIXED WITH EQUAL AMOUNT OF PRECIPITATING AGENT AT 19 C, CRYOPROTECTED WITH 15-20% 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: Sep 14, 2007 / 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: 2.3→30 Å / Num. obs: 84171 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.84 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.41 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 2.3→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODE / Bsol: 29.1693 Å2 / ksol: 0.324567 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Xplor file |
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