+Open data
-Basic information
Entry | Database: PDB / ID: 4ncv | ||||||
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Title | Foldon domain wild type N-conjugate | ||||||
Components | Fibritin | ||||||
Keywords | VIRAL PROTEIN / trimeric scaffold / chemical ligation / folding / trazido-functionalized trimesic acid scaffold | ||||||
Function / homology | Fibritin C-terminal / Fibritin C-terminal region / virion component / Fibritin / Fibritin Function and homology information | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Graewert, M.A. / Berthelmann, A. / Lach, J. / Groll, M. / Eichler, J. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2014 Title: Versatile C(3)-symmetric scaffolds and their use for covalent stabilization of the foldon trimer. Authors: Berthelmann, A. / Lach, J. / Grawert, M.A. / Groll, M. / Eichler, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ncv.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ncv.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ncv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/4ncv ftp://data.pdbj.org/pub/pdb/validation_reports/nc/4ncv | HTTPS FTP |
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-Related structure data
Related structure data | 4ncuSC 4ncwC 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
#1: Protein/peptide | Mass: 3110.499 Da / Num. of mol.: 3 / Fragment: C-terminus fragment (UNP residues 458-484) / Source method: obtained synthetically Details: This sequence occurs naturally in bacteriophage T4 fibritin at its C-terminus and harbors an trimesic acid N-conjugate Source: (synth.) Enterobacteria phage T4 (virus) / References: UniProt: D9IEJ2, UniProt: P10104*PLUS #2: Water | ChemComp-HOH / | Sequence details | A TRIMESIC ACID DERIVATIVE WAS USED TO CROSSLINK THE THREE FOLDON SUBUNITS AT THEIR N-NERMINI. ONLY ...A TRIMESIC ACID DERIVATIVE | |
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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: 2.01 Å3/Da / Density % sol: 38.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.4 M Na/K-phosphate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2013 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. obs: 22182 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.2→1.3 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.3 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NCU Resolution: 1.2→15 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.332 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.039 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.351 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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