[English] 日本語
Yorodumi- PDB-2vjv: Crystal structure of the IS608 transposase in complex with left e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vjv | ||||||
---|---|---|---|---|---|---|---|
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 | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / PROTEIN-DNA COMPLEX / HUH MOTIF / DNA STEM LOOP / TRANSPOSITION | ||||||
Function / homology | Function and homology information transposase activity / DNA transposition / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Barabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vjv.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vjv.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 2vjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vjv ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vjv | HTTPS FTP |
---|
-Related structure data
Related structure data | 2vhgC 2vicC 2vihSC 2vjuC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.985391, 0.170267, -0.003787), Vector: |
-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.) HELICOBACTER PYLORI (bacteria) / Strain: PECAN2A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q933Z0 #2: DNA chain | Mass: 8003.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HELICOBACTER PYLORI (bacteria) #3: DNA chain | Mass: 1783.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HELICOBACTER PYLORI (bacteria) #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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 50.75 % / Description: NONE |
---|---|
Crystal grow | pH: 5 / Details: 6-10% PEG 600 AND 50 MM SODIUM CITRATE PH 5.0 |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.2464 Å2 / ksol: 0.353019 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→24.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|