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Yorodumi- PDB-6qbb: Engineered streptavidin variant (ENAGY) in complex with the Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qbb | ||||||
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Title | Engineered streptavidin variant (ENAGY) 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 / Resolution: 1.52 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 | 6qbb.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qbb.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/6qbb ftp://data.pdbj.org/pub/pdb/validation_reports/qb/6qbb | HTTPS FTP |
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-Related structure data
Related structure data | 6qsyC 6qw4C 6sokC 6sosC 6tipC 1rstS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 15 - 132 / Label seq-ID: 3 - 120
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-Components
#1: Protein | Mass: 13346.434 Da / Num. of mol.: 2 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 #2: Protein/peptide | Mass: 1574.123 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The peptide SAWSHPQFEK carries an anthraniloyl/2-aminobenzoyl (Abz) group at the N-terminus and an amide group at the C-terminus. Source: (synth.) synthetic construct (others) #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: 2.08 Å3/Da / Density % sol: 40.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG MME 550, zinc sulfate, 2-(N-morpholino)ethanesulfonic acid |
-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: 1.52→49.58 Å / Num. obs: 35992 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.039 / Rrim(I) all: 0.085 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.52→1.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.342 / Num. unique obs: 5162 / Rpim(I) all: 0.176 / Rrim(I) all: 0.386 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RST Resolution: 1.52→49.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.721 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 18.109 Å2
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Refinement step | Cycle: 1 / Resolution: 1.52→49.58 Å
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Refine LS restraints |
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