+Open data
-Basic information
Entry | Database: PDB / ID: 1ij8 | |||||||||
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Title | CRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX | |||||||||
Components | AVIDIN | |||||||||
Keywords | UNKNOWN FUNCTION / avidin / streptavidin / pseudo enzymatic activity | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | |||||||||
Authors | Livnah, O. / Huberman, T. | |||||||||
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 | 1ij8.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ij8.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ij8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ij8_validation.pdf.gz | 518.3 KB | Display | wwPDB validaton report |
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Full document | 1ij8_full_validation.pdf.gz | 528.8 KB | Display | |
Data in XML | 1ij8_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1ij8_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ij8 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ij8 | HTTPS FTP |
-Related structure data
Related structure data | 1i9hC 2aviS 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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Details | The second part of the biological assembly to for the avidin tetramer is generated by the two fold axis -x, -y+1, z |
-Components
#1: Protein | Mass: 14350.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: EGG WHITE / References: UniProt: P02701 #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.2 Å3/Da / Density % sol: 43.97 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 12% PEG2000, 0.1M imidazole malate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.3 | ||||||||||||||||||||
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 ULTRAX 18 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 18, 2000 / Details: Max-Flux |
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→50 Å / Num. all: 17510 / Num. obs: 17510 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.279 / % possible all: 98.1 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 98.1 % / Mean I/σ(I) obs: 4.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2AVI Resolution: 2→50 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.204 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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