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- PDB-3wzq: Crystal structure of the core streptavidin mutant V212 (Y22S/N23D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wzq | ||||||
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Title | Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.7 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 | ![]() | 207.9 KB | Display | ![]() |
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PDB format | ![]() | 167 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wznC ![]() 3wzoC ![]() 3wzpC ![]() 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
#1: Protein | Mass: 15310.568 Da / Num. of mol.: 4 / Fragment: UNP residues 37-163 / Mutation: Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZOF / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 60 mM sodium cacodylate trihydrate, 27%(w/v) PEG300, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 57652 / Num. obs: 55926 / % possible obs: 97 % / Redundancy: 5.8 % / Rsym value: 0.054 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.01 / Num. unique all: 57652 / Rsym value: 0.353 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WYQ Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.324 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.119 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.288 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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