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Yorodumi- PDB-5n8t: CRYSTAL STRUCTURE OF STREPTAVIDIN D-amino acid containing peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n8t | |||||||||
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Title | CRYSTAL STRUCTURE OF STREPTAVIDIN D-amino acid containing peptide Gdlwqheatwkkq | |||||||||
Components |
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Keywords | Biotin binding protein / STREPTAVIDIN / BIOTIN BINDING / D-AMINO ACIDS / STREPTAVIDIN PEPTIDE COMPLEX | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | |||||||||
Authors | Lyamichev, V. / Goodrich, L. / Sullivan, E. / Bannen, R. / Benz, J. / Albert, T. / Patel, J. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target. Authors: Lyamichev, V.I. / Goodrich, L.E. / Sullivan, E.H. / Bannen, R.M. / Benz, J. / Albert, T.J. / Patel, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n8t.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n8t.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 5n8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/5n8t ftp://data.pdbj.org/pub/pdb/validation_reports/n8/5n8t | HTTPS FTP |
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-Related structure data
Related structure data | 5n7xC 5n89C 5n8bC 5n8eC 5n8jC 5n8wC 5n99C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 18849.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 |
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#2: Polypeptide(D) | Mass: 1199.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces avidinii (bacteria) |
#3: 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: 1.87 Å3/Da / Density % sol: 34.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1M Sodium citrate pH 4.5, 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.700001 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.700001 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→47.72 Å / Num. obs: 18228 / % possible obs: 100 % / Redundancy: 12.48 % / CC1/2: 0.99 / Rsym value: 0.057 / Net I/σ(I): 14.94 |
Reflection shell | Resolution: 1.61→1.71 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 3098 / CC1/2: 0.341 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→47.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.602 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.671 Å2
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Refinement step | Cycle: 1 / Resolution: 1.61→47.72 Å
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Refine LS restraints |
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