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Yorodumi- PDB-2bgt: CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME BETA-GLUCOSYLTRANSF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bgt | ||||||
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Title | CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME BETA-GLUCOSYLTRANSFERASE IN THE PRESENCE AND ABSENCE OF THE SUBSTRATE URIDINE DIPHOSPHOGLUCOSE | ||||||
Components | BETA-GLUCOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE (GLYCOSYLTRANSFERASE) | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Vrielink, A. / Rueger, W. / Driessen, H.P.C. / Freemont, P.S. | ||||||
Citation | Journal: EMBO J. / Year: 1994 Title: Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose. Authors: Vrielink, A. / Ruger, W. / Driessen, H.P. / Freemont, P.S. #1: Journal: J.Mol.Biol. / Year: 1988 Title: Crystallization and Preliminary X-Ray Studies of T4 Phage Beta-Glucosyltransferase Authors: Freemont, P.S. / Ruger, W. #2: Journal: Nucleic Acids Res. / Year: 1985 Title: T4-Induced Alpha-and Beta-Glucosyltransferase: Cloning of the Genes and a Comparison of Their Products Based on Sequencing Data Authors: Tomaschewski, J. / Gram, H. / Crabb, J.W. / Ruger, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bgt.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bgt.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/2bgt ftp://data.pdbj.org/pub/pdb/validation_reports/bg/2bgt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40719.879 Da / Num. of mol.: 1 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P04547, DNA beta-glucosyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.25 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 5.8 / PH range high: 5.4 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 19074 / % possible obs: 84.3 % / Num. measured all: 52070 / Rmerge(I) obs: 0.084 |
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-Processing
Software |
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Refinement | Resolution: 2.2→10 Å / σ(F): 0 Details: THE COORDINATES ARE PRESENTED IN A COORDINATE FRAME THAT IS TRANSLATED BY 1/4*152.880 ALONG A AND 1/4*52.25 ALONG B. THUS THE TRANSFORMATION PRESENTED ON *SCALE* RECORDS BELOW IS NOT THE DEFAULT.
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.7 Å2 |