+Open data
-Basic information
Entry | Database: PDB / ID: 1i9h | ||||||
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Title | CORE STREPTAVIDIN-BNA COMPLEX | ||||||
Components | STREPTAVIDIN | ||||||
Keywords | UNKNOWN FUNCTION / classical beta barrel / protein-ligand complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Livnah, O. / Huberman, T. / Wilchek, M. / Bayer, E.A. / Eisenberg-Domovich, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Chicken avidin exhibits pseudo-catalytic properties. Biochemical, structural, and electrostatic consequences. Authors: Huberman, T. / Eisenberg-Domovich, Y. / Gitlin, G. / 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 | 1i9h.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i9h.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/1i9h ftp://data.pdbj.org/pub/pdb/validation_reports/i9/1i9h | HTTPS FTP |
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-Related structure data
Related structure data | 1ij8C 2izfS S: Starting model for refinement C: citing same article (ref.) |
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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: 14497.639 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-163 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: 2.04 Å3/Da / Density % sol: 39.56 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% isopropanol, 0.1M NaCitrate, 0.05M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
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 RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 20, 1998 / Details: short Supper Mirrors |
Radiation | Monochromator: Chales Supper short mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 8647 / Num. obs: 8647 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2 % / Rmerge(I) obs: 0.265 / % possible all: 94.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 2 % |
Reflection shell | *PLUS % possible obs: 94.2 % / Mean I/σ(I) obs: 3.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IZF Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0
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Solvent computation | ksol: 0.335388 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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