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Open data
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Basic information
Entry | Database: PDB / ID: 1ixy | ||||||
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Title | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | ||||||
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![]() | TRANSFERASE/DNA / protein-dna complex / base-flipping / abasic site / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lariviere, L. / Morera, S. | ||||||
![]() | ![]() Title: A Base-flipping Mechanism for the T4 Phage beta-Glucosyltransferase and Identification of a Transition-state Analog Authors: Lariviere, L. / Morera, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.8 KB | Display | ![]() |
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PDB format | ![]() | 145.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m5rC ![]() 1jg6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 4 molecules CDEF
#1: DNA chain | Mass: 3890.550 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3941.584 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 40719.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 248 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.51 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, tert-butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Details: Lariviere, L., (2002) Acta Crystallogr., Sect.D, 58, 1484. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 30519 / Num. obs: 30397 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 54.2 Å2 / Rsym value: 0.102 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.5→2.63 Å / Mean I/σ(I) obs: 2.26 / Num. unique all: 4374 / Rsym value: 0.499 / % possible all: 99.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.102 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1JG6 Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |