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Yorodumi- PDB-4pls: Crystal Structures of Designed Armadillo Repeat Proteins: Implica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pls | ||||||
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Title | Crystal Structures of Designed Armadillo Repeat Proteins: Implications of Construct Design and Crystallization Conditions on Overall Structure. | ||||||
Components | Arm00010 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / designed armadillo repeat proteins / protein engineering | ||||||
Function / homology | Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha / ACETATE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Reichen, C. / Madhurantakam, C. / Plueckthun, A. / Mittl, P.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Crystal Structures of Designed Armadillo Repeat Proteins: Implications of Construct Design and Crystallization Conditions on Overall Structure. Authors: Reichen, C. / Madhurantakam, C. / 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 | 4pls.cif.gz | 413.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pls.ent.gz | 340.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/4pls ftp://data.pdbj.org/pub/pdb/validation_reports/pl/4pls | HTTPS FTP |
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-Related structure data
Related structure data | 4plqC 4plrSC 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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Unit cell |
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-Components
#1: Protein | Mass: 29417.791 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: artificial sequence / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-CA / #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25 % PEG 2000-MME, 0.2 M calcium acetate, 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→46.27 Å / Num. obs: 45974 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 44.328 Å2 / Rmerge F obs: 0.118 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.089 / Χ2: 0.946 / Net I/σ(I): 16 / Num. measured all: 242625 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PLR Resolution: 2.35→46.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.492 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 47.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→46.27 Å
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Refine LS restraints |
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