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Yorodumi- PDB-4v3q: Designed armadillo repeat protein with 4 internal repeats, 2nd ge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v3q | ||||||
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Title | Designed armadillo repeat protein with 4 internal repeats, 2nd generation C-cap and 3rd generation N-cap. | ||||||
Components | YIII_M4_AII | ||||||
Keywords | DE NOVO PROTEIN / PROTEIN ENGINEERING / REPEAT PROTEIN / ARMADILLO REPEAT | ||||||
Function / homology | Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha Function and homology information | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Reichen, C. / Madhurantakam, C. / Pluckthun, A. / Mittl, P. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects. Authors: Reichen, C. / Madhurantakam, C. / Hansen, S. / Grutter, M.G. / Pluckthun, A. / Mittl, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v3q.cif.gz | 390.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v3q.ent.gz | 323.9 KB | Display | PDB format |
PDBx/mmJSON format | 4v3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v3q_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 4v3q_full_validation.pdf.gz | 475.2 KB | Display | |
Data in XML | 4v3q_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 4v3q_validation.cif.gz | 62.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/4v3q ftp://data.pdbj.org/pub/pdb/validation_reports/v3/4v3q | HTTPS FTP |
-Related structure data
Related structure data | 4v3oC 4v3rC 4db6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26242.115 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Nonpolymer details | CALCIUM ION (CA): FROM CRYSTALLIZ | |
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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: 2.47 Å3/Da / Density % sol: 50.14 % / Description: NONE |
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Crystal grow | Details: 25 % PEG 2KMME 0.2 M CA-ACETATE 0.1 M NA-ACETATE, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→96.34 Å / Num. obs: 93024 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4db6 Resolution: 1.8→96.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.523 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / 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: 35.499 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→96.34 Å
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Refine LS restraints |
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