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- PDB-2vhg: Crystal Structure of the ISHp608 Transposase in Complex with Righ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vhg | ||||||
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Title | Crystal Structure of the ISHp608 Transposase in Complex with Right End 31-mer DNA | ||||||
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Function / homology | ![]() ![]() ![]() ![]() 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 | ![]() | 91.7 KB | Display | ![]() |
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PDB format | ![]() | 65.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vicC ![]() 2vihC ![]() 2vjuC ![]() 2vjvC ![]() 2a6oS S: Starting model for refinement C: citing same article ( |
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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:
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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: 9543.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() #3: Chemical | ChemComp-MN / | 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: 2.5 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 / Details: 15-20% PEG 3350 AND 0.1 M MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Details: ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE-CRYSTAL (SI220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→40 Å / Num. obs: 13127 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2A6O Resolution: 2.9→40 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 10 Å2 / ksol: 0.221686 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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