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Yorodumi- PDB-4d49: Crystal structure of computationally designed armadillo repeat pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d49 | ||||||
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Title | Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition. | ||||||
Components |
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Keywords | DE NOVO PROTEIN/PEPTIDE / DE NOVO PROTEIN-PEPTIDE COMPLEX | ||||||
Function / homology | Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha / ARGININE Function and homology information | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Reichen, C. / Forzani, C. / Zhou, T. / Parmeggiani, F. / Fleishman, S.J. / Mittl, P.R.E. / Madhurantakam, C. / Honegger, A. / Ewald, C. / Zerbe, O. ...Reichen, C. / Forzani, C. / Zhou, T. / Parmeggiani, F. / Fleishman, S.J. / Mittl, P.R.E. / Madhurantakam, C. / Honegger, A. / Ewald, C. / Zerbe, O. / Baker, D. / Caflisch, A. / Pluckthun, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. Authors: Reichen, C. / Forzani, C. / Zhou, T. / Parmeggiani, F. / Fleishman, S.J. / Mittl, P.R.E. / Madhurantakam, C. / Honegger, A. / Ewald, C. / Zerbe, O. / Baker, D. / Caflisch, A. / Pluckthun, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d49.cif.gz | 374.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d49.ent.gz | 311.8 KB | Display | PDB format |
PDBx/mmJSON format | 4d49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d49_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 4d49_full_validation.pdf.gz | 486.8 KB | Display | |
Data in XML | 4d49_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 4d49_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/4d49 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/4d49 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 12 - 249 / Label seq-ID: 5 - 242
NCS ensembles :
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-Components
#1: Protein | Mass: 25851.041 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: COMPUTATIONALLY DESIGNED ARMADILLO REPEAT PROTEIN IN COMPLEX WITH A PEPTIDE Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: DE NOVO DESIGNED PROTEIN / Plasmid: YIII_(DQ_V1)4_C(PAF) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE #2: Protein/peptide | Mass: 1589.953 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: DE NOVO DESIGNED PROTEIN / Plasmid: YIII_(DQ_V1)4_C(PAF) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE #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: 2.39 Å3/Da / Density % sol: 48.48 % / Description: DATA WERE COLLECTED USING THE ROTATION METHOD |
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED AT PH 8.5 / 0.2M MAGNESIUM CHLORIDE / 0.1 M TRIS HCL / 10 % W/V PEG 8000 / 10 % W/V PEG 1000. PRIOR TO CRYSTALLIZATION, 1.5 MOLAR EXCESS OF PEPTIDE (RR)5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→20 Å / Num. obs: 106706 / % possible obs: 95.7 % / Observed criterion σ(I): 1.37 / Redundancy: 2.26 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.01 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.32 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.37 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ARM00016 Resolution: 2.09→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.082 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 43.459 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→20 Å
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Refine LS restraints |
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