+Open data
-Basic information
Entry | Database: PDB / ID: 1lcv | ||||||
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Title | streptavidin-norbiotin complex | ||||||
Components | streptavidin | ||||||
Keywords | UNKNOWN FUNCTION / avidin / streptavidin / biotin / biotin-analogues | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Livnah, O. / Pazy, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Ligand exchange between proteins: exchange of biotin and biotin derivatives between avidin and streptavidin Authors: Pazy, Y. / Kulik, T. / Bayer, E.A. / Wilchek, M. / Livnah, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lcv.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lcv.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 1lcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lcv ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lcv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: -x,y -z |
-Components
#1: Protein | Mass: 12764.833 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: Chemical | #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: 2.32 Å3/Da / Density % sol: 47.06 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 1.2 M ammonium sulfate, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.8 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1999 / Details: short supper mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 10095 / % possible obs: 92.2 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 93.4 |
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 2 % / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS % possible obs: 93.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.188 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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