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Yorodumi- PDB-1j39: Crystal Structure of T4 phage BGT in complex with its UDP-glucose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j39 | ||||||
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Title | Crystal Structure of T4 phage BGT in complex with its UDP-glucose substrate | ||||||
Components | DNA beta-glucosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase / GT-B / UDP-glucose | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Lariviere, L. / Morera, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal structures of the T4 phage beta-glucosyltransferase and the D100A mutant in complex with UDP-glucose: glucose binding and identification of the catalytic base for a direct displacement mechanism. Authors: Lariviere, L. / Gueguen-Chaignon, V. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j39.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j39.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 1j39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j39_validation.pdf.gz | 759.3 KB | Display | wwPDB validaton report |
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Full document | 1j39_full_validation.pdf.gz | 769.6 KB | Display | |
Data in XML | 1j39_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 1j39_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j39 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j39 | HTTPS FTP |
-Related structure data
Related structure data | 1nvkC 1nzdC 1nzfC 2bgtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a monomer |
-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 / Gene: BGT / Plasmid: pBSK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P04547, DNA beta-glucosyltransferase | ||
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#2: Chemical | ChemComp-UPG / | ||
#3: Chemical | #4: 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: 2.29 Å3/Da / Density % sol: 45.95 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
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: ESRF / Beamline: BM14 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 11, 2002 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.87→20 Å / Num. all: 34553 / Num. obs: 34069 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.047 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.87→1.94 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 3391 / Rsym value: 0.239 / % possible all: 96.3 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 34078 / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS % possible obs: 96.3 % / Rmerge(I) obs: 0.239 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BGT Resolution: 1.87→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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