+Open data
-Basic information
Entry | Database: PDB / ID: 2a6m | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the ISHp608 Transposase | ||||||
Components | ISHp608 transposase | ||||||
Keywords | TRANSCRIPTION/DNA / RNA Recognition Motif / TRANSCRIPTION-DNA COMPLEX | ||||||
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 / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Ronning, D.R. / Guynet, C. / Ton-Hoang, B. / Perez, Z.N. / Ghirlando, R. / Chandler, M. / Dyda, F. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: Active site sharing and subterminal hairpin recognition in a new class of DNA transposases. Authors: Ronning, D.R. / Guynet, C. / Ton-Hoang, B. / Perez, Z.N. / Ghirlando, R. / Chandler, M. / Dyda, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a6m.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a6m.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a6m_validation.pdf.gz | 373.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2a6m_full_validation.pdf.gz | 391.1 KB | Display | |
Data in XML | 2a6m_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2a6m_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/2a6m ftp://data.pdbj.org/pub/pdb/validation_reports/a6/2a6m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biologically relevant molecule is the dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 18106.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: pDR32B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q933Z0 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, Sodium Thiocyanate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 12555 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 28.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.4→22.8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1105901.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.6966 Å2 / ksol: 0.297548 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.6 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→22.8 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|