+Open data
-Basic information
Entry | Database: PDB / ID: 6xg8 | ||||||
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Title | ISCth4 transposase, pre-cleaved complex, PCC | ||||||
Components |
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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 / MAD / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xg8.cif.gz | 234 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xg8.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 6xg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/6xg8 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/6xg8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-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: 7914.155 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: 8056.225 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) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 71 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, sodium chloride, sodium acetate, PEG4000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2017 |
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→29.61 Å / Num. obs: 20108 / % possible obs: 99.5 % / Redundancy: 7.17 % / Biso Wilson estimate: 148.31 Å2 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 3.5→3.59 Å / Redundancy: 7.51 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1474 / CC1/2: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.5→29.61 Å / SU ML: 0.5551 / Cross valid method: THROUGHOUT / σ(F): 1.8 / Phase error: 35.7569 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 167.34 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→29.61 Å
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Refine LS restraints |
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LS refinement shell |
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