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Yorodumi- PDB-1sxq: BGT in complex with a 13mer DNA containing a central C:G base pai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sxq | ||||||
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Title | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / flipped-out base / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA beta-glucosyltransferase / DNA beta-glucosyltransferase activity / symbiont-mediated evasion of host restriction-modification system / DNA modification Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lariviere, L. / Morera, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural evidence of a passive base flipping mechanism for {beta}-Glucosyltransferase Authors: Lariviere, L. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sxq.cif.gz | 207.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sxq.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 1sxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/1sxq ftp://data.pdbj.org/pub/pdb/validation_reports/sx/1sxq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3988.646 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3948.622 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 40719.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: BGT, BETA-GT / Production host: Escherichia coli (E. coli) / References: UniProt: P04547, DNA beta-glucosyltransferase #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 5000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2002 / Details: 0.97 |
Radiation | Monochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 90030 / Num. obs: 90030 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.059 / Net I/σ(I): 2 |
Reflection shell | Resolution: 1.8→1.86 Å / Rsym value: 0.336 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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