+Open data
-Basic information
Entry | Database: PDB / ID: 1nbx | ||||||
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Title | Streptavidin Mutant Y43A at 1.70A Resolution | ||||||
Components | Streptavidin | ||||||
Keywords | BIOTIN-BINDING PROTEIN / tetramer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / isomorphous / Resolution: 1.7 Å | ||||||
Authors | Le Trong, I. / Freitag, S. / Klumb, L.A. / Chu, V. / Stayton, P.S. / Stenkamp, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nbx.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nbx.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nbx_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 1nbx_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 1nbx_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1nbx_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nbx ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nbx | HTTPS FTP |
-Related structure data
Related structure data | 1n43C 1n4jC 1n7yC 1n9mC 1n9yC 1nc9C 1ndjC 1swaS C: citing same article (ref.) S: Starting model for refinement |
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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: 13189.239 Da / Num. of mol.: 4 / Fragment: core streptavidin, residues 13-139 / Mutation: Y43A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Gene: core streptavidin / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22629 #2: Chemical | ChemComp-MRD / ( | #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: 2.03 Å3/Da / Density % sol: 39.4 % | |||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: MPD, pH 4.5, 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: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 29, 1996 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 43743 / Num. obs: 43743 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 43769 / % possible obs: 86 % / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 35 % / Rmerge(I) obs: 0.41 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous Starting model: 1SWA Resolution: 1.7→10 Å / Num. parameters: 14551 / Num. restraintsaints: 14614 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 3270 / Occupancy sum non hydrogen: 3634 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→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: 1.7 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.211 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |