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Yorodumi- PDB-6qsy: Engineered streptavidin variant (H--WY) in complex with the Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qsy | ||||||
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Title | Engineered streptavidin variant (H--WY) in complex with the Strep-tag II peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / LOOP ENGINEERING / PROTEIN ENGINEERING / STREP-TAG / STREPTAVIDIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Skerra, A. / Eichinger, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2021 Title: The Role of Changing Loop Conformations in Streptavidin Versions Engineered for High-affinity Binding of the Strep-tag II Peptide. Authors: Schmidt, T.G.M. / Eichinger, A. / Schneider, M. / Bonet, L. / Carl, U. / Karthaus, D. / Theobald, I. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qsy.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qsy.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/6qsy ftp://data.pdbj.org/pub/pdb/validation_reports/qs/6qsy | HTTPS FTP |
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-Related structure data
Related structure data | 6qbbC 6qw4C 6sokC 6sosC 6tipC 1rstS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13299.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: engineered protein / Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 | ||||
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#2: Protein/peptide | Mass: 1335.445 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide SAWSHPQFEK carries an anthraniloyl/2-aminobenzoyl (BE2) group at the N-terminus and an amide at the C-terminus. Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | #4: Chemical | ChemComp-TRS / | #5: 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: 2.55 Å3/Da / Density % sol: 51.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: polyethylene glycol 8000, lithium sulfate, tris(hydroxymethyl)aminomethane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2013 / Details: Si mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→54.415 Å / Num. obs: 16563 / % possible obs: 100 % / Redundancy: 9.5 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.068 / Rsym value: 0.064 / Net I/av σ(I): 8.5 / Net I/σ(I): 22 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RST Resolution: 1.7→54.415 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.876 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0867 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.082 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.06 Å2 / Biso mean: 19.423 Å2 / Biso min: 6.37 Å2
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Refinement step | Cycle: final / Resolution: 1.7→54.415 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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