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- PDB-2vjv: Crystal structure of the IS608 transposase in complex with left e... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vjv | ||||||
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Title | Crystal structure of the IS608 transposase in complex with left end 26-mer DNA hairpin and a 6-mer DNA representing the left end cleavage site | ||||||
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![]() | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / PROTEIN-DNA COMPLEX / HUH MOTIF / DNA STEM LOOP / TRANSPOSITION | ||||||
Function / homology | ![]() transposase activity / DNA transposition / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Barabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F. | ||||||
![]() | ![]() Title: Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection. Authors: Barabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.7 KB | Display | ![]() |
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PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 256.2 KB | Display | ![]() |
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Full document | ![]() | 326.6 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vhgC ![]() 2vicC ![]() 2vihSC ![]() 2vjuC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.985391, 0.170267, -0.003787), Vector: |
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Components
#1: Protein | Mass: 18392.430 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 8003.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: DNA chain | Mass: 1783.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE ADDITION OF THE FIRST 5 RESIDUES (GSAMA) TO THE DATABASE SEQUENCE ARE THE RESULT OF CLONING ARTIFACT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 50.75 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 6-10% PEG 600 AND 50 MM SODIUM CITRATE PH 5.0 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 12, 2007 / Details: MULTILAYER FOCUSING OPTICS |
Radiation | Monochromator: MULTILAYER FOCUSING MIRROR / 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→40 Å / Num. obs: 38044 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.6 / % possible all: 64.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VIH Resolution: 1.9→24.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1368904.85 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.2464 Å2 / ksol: 0.353019 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
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Xplor file |
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