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Open data
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Basic information
Entry | Database: PDB / ID: 8ant | ||||||
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Title | Crystal structure of 6xhis-tagged phi3T_93 protein | ||||||
![]() | YopN, Phi3T_93 | ||||||
![]() | VIRAL PROTEIN / Arbitrium / Phi3T / lysis-lysogeny decission | ||||||
Function / homology | metal ion binding / 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 | ![]() | 91 KB | Display | ![]() |
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PDB format | ![]() | 61.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.4 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8anuC ![]() 8anvC ![]() 8c8eC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.999998999312, -0.00131241290325, 0.000528155320264), (-0.00126968177914, 0.997251556147, 0.0740791581419), (-0.000623926158028, 0.0740784134226, -0.997252224556) ...NCS oper: (Code: given Matrix: (-0.999998999312, -0.00131241290325, 0.000528155320264), Vector: |
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Components
#1: Protein | Mass: 12239.717 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.58 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris pH8, 5% glycerol, 0.6M Na/K tartrate |
-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: Sep 17, 2021 |
Radiation | Monochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50.83 Å / Num. obs: 16124 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 34.06 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.382 / Num. unique obs: 1017 / CC1/2: 0.975 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.9→37.2 Å / SU ML: 0.2875 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.7673 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→37.2 Å
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Refine LS restraints | Type: f_dihedral_angle_d / Dev ideal: 5.6902 / Number: 179 | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.491121930325 Å | ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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