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Yorodumi- PDB-1c3j: T4 PHAGE BETA-GLUCOSYLTRANSFERASE: SUBSTRATE BINDING AND PROPOSED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c3j | ||||||
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Title | T4 PHAGE BETA-GLUCOSYLTRANSFERASE: SUBSTRATE BINDING AND PROPOSED CATALYTIC MECHANISM | ||||||
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 / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.88 Å | ||||||
Authors | Morera, S. / Imberty, A. / Aschke-Sonnenborn, U. / Ruger, W. / Freemont, P.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism. Authors: Morera, S. / Imberty, A. / Aschke-Sonnenborn, U. / Ruger, W. / Freemont, P.S. #1: 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.C. / Freemont, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c3j.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3j.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c3j_validation.pdf.gz | 744 KB | Display | wwPDB validaton report |
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Full document | 1c3j_full_validation.pdf.gz | 748.3 KB | Display | |
Data in XML | 1c3j_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1c3j_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3j ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3j | HTTPS FTP |
-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: Chemical | ChemComp-UDP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: AMMONIUM SULFATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 5.8 / PH range high: 5.4 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→26 Å / Num. all: 223460 / Num. obs: 31888 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 19.659 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 3 % / Rmerge(I) obs: 0.278 / % possible all: 71 |
Reflection | *PLUS Num. measured all: 223460 |
Reflection shell | *PLUS % possible obs: 71 % |
-Processing
Software |
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Refinement | Resolution: 1.88→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.88→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.67 Å2 |