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Yorodumi- PDB-4zv6: Crystal structure of the artificial alpharep-7 octarellinV.1 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zv6 | ||||||
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Title | Crystal structure of the artificial alpharep-7 octarellinV.1 complex | ||||||
Components |
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Keywords | DE NOVO PROTEIN / synthetic gene / artificial protein / Rossmann-like | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.22 Å | ||||||
Authors | Figueroa, M. / Sleutel, M. / Urvoas, A. / Valerio-Lepiniec, M. / Minard, P. / Martial, J.A. / van de Weerdt, C. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2016 Title: The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools. Authors: Figueroa, M. / Sleutel, M. / Vandevenne, M. / Parvizi, G. / Attout, S. / Jacquin, O. / Vandenameele, J. / Fischer, A.W. / Damblon, C. / Goormaghtigh, E. / Valerio-Lepiniec, M. / Urvoas, A. / ...Authors: Figueroa, M. / Sleutel, M. / Vandevenne, M. / Parvizi, G. / Attout, S. / Jacquin, O. / Vandenameele, J. / Fischer, A.W. / Damblon, C. / Goormaghtigh, E. / Valerio-Lepiniec, M. / Urvoas, A. / Durand, D. / Pardon, E. / Steyaert, J. / Minard, P. / Maes, D. / Meiler, J. / Matagne, A. / Martial, J.A. / Van de Weerdt, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zv6.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zv6.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zv6_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 4zv6_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 4zv6_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4zv6_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zv6 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zv6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32362.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 |
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#2: Protein | Mass: 24867.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pJB122 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21% (w/v) PEG400, 100mM MgCl2, 100mM Hepes pH 7.5, 20mg/ml octarellin-alpha rep complex |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→47.1 Å / Num. obs: 24372 / % possible obs: 98.8 % / Redundancy: 3.7 % / Net I/σ(I): 16.15 |
-Processing
Software |
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Refinement | Resolution: 2.22→47.097 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→47.097 Å
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Refine LS restraints |
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LS refinement shell |
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