+Open data
-Basic information
Entry | Database: PDB / ID: 6xgw | ||||||
---|---|---|---|---|---|---|---|
Title | ISCth4 transposase, pre-reaction complex, PRC | ||||||
Components |
| ||||||
Keywords | RECOMBINATION / antibiotic resistance / promoter / transposon | ||||||
Function / homology | Transposase, mutator type / Transposase, Mutator family / Transposases, Mutator family, signature. / transposase activity / DNA transposition / DNA binding / DNA / DNA (> 10) / Mutator family transposase Function and homology information | ||||||
Biological species | Hungateiclostridium thermocellum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Kosek, D. / Dyda, F. | ||||||
Citation | Journal: Embo J. / Year: 2021 Title: Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition. Authors: Kosek, D. / Hickman, A.B. / Ghirlando, R. / He, S. / Dyda, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6xgw.cif.gz | 202.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xgw.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xgw_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6xgw_full_validation.pdf.gz | 462.3 KB | Display | |
Data in XML | 6xgw_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 6xgw_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/6xgw ftp://data.pdbj.org/pub/pdb/validation_reports/xg/6xgw | HTTPS FTP |
-Related structure data
Related structure data | 6xg8SC 6xgxC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47498.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria) Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372 Gene: Cthe_0148, Cthe_0356, Cthe_0371, Cthe_1193, Cthe_1874, Cthe_3051 Production host: Escherichia coli (E. coli) / References: UniProt: A3DBR0 #2: DNA chain | | Mass: 9769.370 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria) #3: DNA chain | | Mass: 9906.394 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria) |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 61 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium cacodylate, calcium chloride, ammonium acetate, PEG4000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→46.07 Å / Num. obs: 17976 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 134.67 Å2 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.097 / Net I/σ(I): 10.94 |
Reflection shell | Resolution: 3.5→3.59 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 1323 / CC1/2: 0.799 / % possible all: 99.66 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6XG8 Resolution: 3.5→29.48 Å / SU ML: 0.5344 / Cross valid method: THROUGHOUT / σ(F): 1.78 / Phase error: 36.8918 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 154.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→29.48 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|