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Open data
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Basic information
Entry | Database: PDB / ID: 1ndj | ||||||
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Title | Streptavidin Mutant Y43F with Biotin at 1.81A Resolution | ||||||
![]() | Streptavidin | ||||||
![]() | BIOTIN-BINDING PROTEIN / tetramer | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Le Trong, I. / Freitag, S. / Klumb, L.A. / Chu, V. / Stayton, P.S. / Stenkamp, R.E. | ||||||
![]() | ![]() Title: Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin. Authors: Le Trong, I. / Freitag, S. / Klumb, L.A. / Chu, V. / Stayton, P.S. / Stenkamp, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.9 KB | Display | ![]() |
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PDB format | ![]() | 80 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.5 KB | Display | ![]() |
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Full document | ![]() | 466.5 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n43C ![]() 1n4jC ![]() 1n7yC ![]() 1n9mC ![]() 1n9yC ![]() 1nbxC ![]() 1nc9C ![]() 1sweS 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: 13265.336 Da / Num. of mol.: 4 / Fragment: core streptavidin, residues 13-139 / Mutation: Y43F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-BTN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 46.83 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→99 Å / Num. all: 35211 / Num. obs: 35211 / % possible obs: 79.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Highest resolution: 1.8 Å / % possible obs: 80 % / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 30 % / Rmerge(I) obs: 0.32 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS Starting model: 1SWE Resolution: 1.81→10 Å / Num. parameters: 15159 / Num. restraintsaints: 15067 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 3328 / Occupancy sum non hydrogen: 3789 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.227 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |