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Yorodumi- PDB-2ru4: Designed Armadillo Repeat Protein Self-ASsembled Complex (YIIM2-MAII) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ru4 | ||||||
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Title | Designed Armadillo Repeat Protein Self-ASsembled Complex (YIIM2-MAII) | ||||||
Components |
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Keywords | DE NOVO PROTEIN / solenoid repeat / Armadillo repeat motif / self-assembly / solution complex | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Model details | closest to the average, model1 | ||||||
Authors | Zerbe, O. / Christen, M.T. / Plueckthun, A. / Watson, R.P. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure Authors: Watson, R.P. / Christen, M.T. / Ewald, C. / Bumbak, F. / Reichen, C. / Mihajlovic, M. / Schmidt, E. / Guntert, P. / Caflisch, A. / Pluckthun, A. / Zerbe, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ru4.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2ru4.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2ru4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/2ru4 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/2ru4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12193.524 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): M15 |
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#2: Protein | Mass: 9104.069 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): M15 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Solution structure of the complex formed in solution by a split Armadillo repeat protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: CHAINS A AND B ARE NOT COVALENTLY LINKED. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 150 / pH: 7.4 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 Details: Structure calculation in vacuo, Refinement in explicit TIP3P water | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1958 / NOE intraresidue total count: 531 / NOE long range total count: 404 / NOE medium range total count: 498 / NOE sequential total count: 525 / Protein phi angle constraints total count: 138 / Protein psi angle constraints total count: 141 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.06 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 3.67 ° / Maximum upper distance constraint violation: 0.466 Å / Representative conformer: 1 / Torsion angle constraint violation method: PDBSTAT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0323 Å / Distance rms dev error: 0.0011 Å |