[English] 日本語
![](img/lk-miru.gif)
- PDB-2vju: Crystal structure of the IS608 transposase in complex with the co... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2vju | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the IS608 transposase in complex with the complete Right end 35-mer DNA and manganese | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN / PROTEIN-DNA COMPLEX / DNA-BINDING PROTEIN / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 109.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 79.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 465 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vhgC ![]() 2vicC ![]() 2vihSC ![]() 2vjvC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: Protein | Mass: 18392.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 10802.956 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | BASES DC C -3, DG C -35 AND DG C -9 FORM A BASE TRIPLET BASES DT C -4, DA C -34 AND DA C -10 FORM A ...BASES DC C -3, DG C -35 AND DG C -9 FORM A BASE TRIPLET BASES DT C -4, DA C -34 AND DA C -10 FORM A BASE TRIPLET BASES DC D -3, DG D -35 AND DG D -9 FORM A BASE TRIPLET BASES DT D -4, DA D -34 AND DA D -10 FORM A BASE TRIPLET | Sequence details | THE ADDITION OF THE FIRST 5 RESIDUES (GSAMA) TO THE DATABASE SEQUENCE ARE THE RESULT OF CLONING ARTIFACT | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 52 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: 20-25% PEG 3350, 0.1 M MES PH 5.5, AND 0.1 M AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 20, 2006 / Details: MULTILAYER FOCUSING MIRROR |
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: 2.4→50 Å / Num. obs: 22916 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.7 / % possible all: 94.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VIH Resolution: 2.4→20.04 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.5054 Å2 / ksol: 0.335087 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: ION.TOP |