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- PDB-3wzo: Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wzo | ||||||
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Title | Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin long tail (BTNtail) at 1.5 A resolution | ||||||
![]() | Streptavidin | ||||||
![]() | BIOTIN BINDING PROTEIN / beta-barrel | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Tsumoto, K. / Kodama, T. ...Kawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Tsumoto, K. / Kodama, T. / Kanai, M. / Doi, H. / Inoue, T. / Sugiyama, A. | ||||||
![]() | ![]() Title: Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. Authors: Kawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Kodama, T. / Kanai, M. / Doi, H. / Inoue, T. / Sugiyama, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216.6 KB | Display | ![]() |
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PDB format | ![]() | 172.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wznC ![]() 3wzpC ![]() 3wzqC ![]() 3wyqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 13227.240 Da / Num. of mol.: 4 / Fragment: UNP residues 37-163 / Mutation: Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 251 molecules ![](data/chem/img/ZOE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZOE / #3: Chemical | #4: Chemical | ChemComp-CD / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M cadmium chloride hydrate, 0.1 M sodium acetate trihydrate, 30%(v/v) PEG400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 65724 / Num. obs: 64012 / % possible obs: 97.4 % / Redundancy: 6.3 % / Rsym value: 0.035 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.08 / Num. unique all: 64012 / Rsym value: 0.232 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WYQ Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.107 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.935 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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