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Yorodumi- PDB-5aqa: DARPin-based Crystallization Chaperones exploit Molecular Geometr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aqa | |||||||||
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Title | DARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography | |||||||||
Components | OFF7_DB04V3 | |||||||||
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: 2.6 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 | 5aqa.cif.gz | 453.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aqa.ent.gz | 386.7 KB | Display | PDB format |
PDBx/mmJSON format | 5aqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aqa_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 5aqa_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 5aqa_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 5aqa_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/5aqa ftp://data.pdbj.org/pub/pdb/validation_reports/aq/5aqa | HTTPS FTP |
-Related structure data
Related structure data | 5aq7C 5aq8C 5aq9C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45371.645 Da / Num. of mol.: 2 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 #2: Chemical | ChemComp-SCN / #3: 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: 2.73 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 8 Details: PEG6000 17% W/V, AMMONIUM CHLORIDE 0.2 M, HEPES 0.05 M, PH 7.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00721 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 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: 1.00721 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47 Å / Num. obs: 31359 / % possible obs: 99.8 % / Observed criterion σ(I): 0.4 / Redundancy: 10 % / Biso Wilson estimate: 61.93 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 11.14 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 0.32 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3DTM AND 1SVX CHAIN A Resolution: 2.6→47.089 Å / SU ML: 0.46 / σ(F): 1.99 / Phase error: 32.57 / 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: 84.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→47.089 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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