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- PDB-5v2o: De Novo Design of Novel Covalent Constrained Meso-size Peptide Sc... -
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Open data
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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 | ||||||
![]() | TP2 | ||||||
![]() | DE NOVO PROTEIN / De Novo Design / Covalent core / constrained mess-size peptide | ||||||
Function / homology | 1,3,5-BENZENETRICARBOXYLIC ACID![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Dang, B. / Wu, H. / Mulligan, V.K. / Mravic, M. / Wu, Y. / Lemmin, T. / Ford, A. / Silva, D. / Baker, D. / DeGrado, W.F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.6 KB | Display | ![]() |
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PDB format | ![]() | 142.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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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 ![](data/chem/img/SO4.gif)
![](data/chem/img/2PE.gif)
![](data/chem/img/TMM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/2PE.gif)
![](data/chem/img/TMM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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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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