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Open data
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Basic information
Entry | Database: PDB / ID: 8anu | ||||||
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Title | Crystal structure of protein phi3T-93 | ||||||
![]() | YopN. Phi3T_93 | ||||||
![]() | VIRAL PROTEIN / Arbitrium / Phi3T / lysis-lysogeny decission | ||||||
Function / homology | metal ion binding / NICKEL (II) ION / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zamora-Caballero, S. / Marina, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Antagonistic interactions between phage and host factors control arbitrium lysis-lysogeny decision. Authors: Zamora-Caballero, S. / Chmielowska, C. / Quiles-Puchalt, N. / Brady, A. / Del Sol, F.G. / Mancheno-Bonillo, J. / Felipe-Ruiz, A. / Meijer, W.J.J. / Penades, J.R. / Marina, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
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PDB format | ![]() | 51.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8antSC ![]() 8anvC ![]() 8c8eC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Components
#1: Protein | Mass: 9768.052 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.15 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop Details: 10%PEG8000, 50mM magnesium acetate, 100mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2021 |
Radiation | Monochromator: Channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→43.47 Å / Num. obs: 6697 / % possible obs: 98.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 33.4114979572 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.31→2.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 985 / CC1/2: 0.961 / Rpim(I) all: 0.102 / Rrim(I) all: 0.237 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8ANT Resolution: 2.31014705408→40.06302883 Å / SU ML: 0.252471672262 / Cross valid method: FREE R-VALUE / σ(F): 1.33786559852 / Phase error: 28.1250642639
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.1353823492 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31014705408→40.06302883 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31015→2.9104 Å
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