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Yorodumi- PDB-5n8w: CRYSTAL STRUCTURE OF STREPTAVIDIN with D-amino acid containing pe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n8w | ||||||
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Title | CRYSTAL STRUCTURE OF STREPTAVIDIN with D-amino acid containing peptide GGwhdeatwkpG | ||||||
Components |
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Keywords | biotin binding protein / STREPTAVIDIN / BIOTIN BINDING / D-AMINO ACIDS / STREPTAVIDIN PEPTIDE COMPLEX / STREPTAVIDIN PEPTIDE 11101 COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 | 5n8w.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n8w.ent.gz | 107.9 KB | Display | PDB format |
PDBx/mmJSON format | 5n8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n8w_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 5n8w_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 5n8w_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 5n8w_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/5n8w ftp://data.pdbj.org/pub/pdb/validation_reports/n8/5n8w | HTTPS FTP |
-Related structure data
Related structure data | 5n7xC 5n89C 5n8bC 5n8eC 5n8jC 5n8tC 5n99C 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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-Components
#1: Protein | Mass: 18849.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 #2: Polypeptide(D) | Mass: 1617.739 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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: 1.87 Å3/Da / Density % sol: 34.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Magnesium acetate 0.1M MOPS pH 7.5 12% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→62.3 Å / Num. obs: 122566 / % possible obs: 99.2 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 5.29 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.01 / Num. unique obs: 28666 / CC1/2: 0.792 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→62.3 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.639 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / 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: 11.811 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→62.3 Å
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Refine LS restraints |
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