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Yorodumi- PDB-5aq8: DARPin-based Crystallization Chaperones exploit Molecular Geometr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aq8 | ||||||
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Title | DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography | ||||||
Components | OFF7_DB12V4 | ||||||
Keywords | CHAPERONE / CRYSTALLIZATION CHAPERONE / DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) / RIGID DOMAIN FUSION | ||||||
Function / homology | Ankyrin repeat-containing domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / THIOCYANATE ION Function and homology information | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Darpin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography Authors: Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aq8.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aq8.ent.gz | 198.7 KB | Display | PDB format |
PDBx/mmJSON format | 5aq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/5aq8 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/5aq8 | HTTPS FTP |
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-Related structure data
Related structure data | 5aq7C 5aq9C 5aqaC 5aqbC 1svxS 3dtmS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45962.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.7 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PEG4000 18.3 %, KSCN 0.286 M, HEPES-NA, 0.1 M, PH 7.5 |
-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: Nov 24, 2011 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR |
Radiation | Monochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→43.72 Å / Num. obs: 43423 / % possible obs: 1 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 18.64 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.13 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.51 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3DTM AND 1SVX CHAIN A Resolution: 1.62→43.717 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 26.86 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→43.717 Å
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Refine LS restraints |
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LS refinement shell |
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