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Yorodumi- PDB-5v2o: De Novo Design of Novel Covalent Constrained Meso-size Peptide Sc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v2o | ||||||
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Title | De Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique Tertiary Structures | ||||||
Components | TP2 | ||||||
Keywords | DE NOVO PROTEIN / De Novo Design / Covalent core / constrained mess-size peptide | ||||||
Function / homology | 1,3,5-BENZENETRICARBOXYLIC ACID Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.2 Å | ||||||
Authors | Dang, B. / Wu, H. / Mulligan, V.K. / Mravic, M. / Wu, Y. / Lemmin, T. / Ford, A. / Silva, D. / Baker, D. / DeGrado, W.F. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures. Authors: Dang, B. / Wu, H. / Mulligan, V.K. / Mravic, M. / Wu, Y. / Lemmin, T. / Ford, A. / Silva, D.A. / Baker, D. / DeGrado, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v2o.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v2o.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 5v2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/5v2o ftp://data.pdbj.org/pub/pdb/validation_reports/v2/5v2o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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6 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 6190.015 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: De novo designed molecule / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 377 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-2PE / #4: Chemical | ChemComp-TMM / #5: Chemical | #6: 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: 2.6 Å3/Da / Density % sol: 52.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, pH 6.5, 2.0 M ((NH4)2SO4 , 5 %w/v PEG 400,Protein: 10mg/mL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.82648 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82648 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→54.81 Å / Num. obs: 127440 / % possible obs: 92.4 % / Redundancy: 3 % / CC1/2: 0.99 / Net I/σ(I): 7.8 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.2→54.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.363 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 20.247 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→54.8 Å
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Refine LS restraints |
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