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Yorodumi- PDB-1y8z: alpha-glucosyltransferase in complex with UDP and a 13-mer DNA co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y8z | ||||||
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Title | alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a HMU base at 1.9 A resolution | ||||||
Components |
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Keywords | Transferase/DNA / Transferase / Transferase-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA alpha-glucosyltransferase / DNA alpha-glucosyltransferase activity / symbiont-mediated suppression of host CRISPR-cas system / symbiont-mediated suppression of host adaptive immune response / symbiont-mediated evasion of host restriction-modification system / DNA modification / virus-mediated perturbation of host defense response Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Lariviere, L. / Sommer, N. / Morera, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase. Authors: Lariviere, L. / Sommer, N. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y8z.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y8z.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 1y8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y8z_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1y8z_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1y8z_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 1y8z_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y8z ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y8z | HTTPS FTP |
-Related structure data
Related structure data | 1xv5C 1y6fSC 1y6gC 1ya6C C: citing same article (ref.) S: Starting model for refinement |
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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
-DNA chain , 2 types, 2 molecules CD
#1: DNA chain | Mass: 4030.647 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 47062.426 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 / Plasmid: proExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): XL1blue / References: UniProt: P04519, DNA alpha-glucosyltransferase |
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-Non-polymers , 5 types, 506 molecules
#4: Chemical | ChemComp-NCO / #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / | #8: 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: 2.1 Å3/Da / Density % sol: 41.6 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG10000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 23, 2004 |
Radiation | Monochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 62948 / Num. obs: 62256 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.058 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.45 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y6F Resolution: 1.9→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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