+Open data
-Basic information
Entry | Database: PDB / ID: 7zn1 | ||||||
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Title | Avidin + Biotin-Tempo | ||||||
Components | Avidin | ||||||
Keywords | PROTEIN BINDING / Avidin / Biotin / TEMPO free radical | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Milani, J. / Lau, K. / Pojer, F. / Ansermet, J.P. / Saenz, F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Avidin + Biotin-Tempo Authors: Milani, J. / Lau, K. / Pojer, F. / Ansermet, J.P. / Saenz, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zn1.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zn1.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 7zn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zn1_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7zn1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7zn1_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 7zn1_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/7zn1 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/7zn1 | HTTPS FTP |
-Related structure data
Related structure data | 7zylC 1ravS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 16787.193 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02701 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar |
-Non-polymers , 4 types, 55 molecules
#4: Chemical | ChemComp-KFL / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | 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: 1.91 Å3/Da / Density % sol: 35.46 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Zinc Acetate dihydrate 22% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→44.5 Å / Num. obs: 40645 / % possible obs: 95.9 % / Redundancy: 2.13 % / Biso Wilson estimate: 44.79 Å2 / CC1/2: 0.995 / Net I/σ(I): 5.13 |
Reflection shell | Resolution: 2.33→2.48 Å / Num. unique obs: 6570 / CC1/2: 0.609 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1rav Resolution: 2.33→44.5 Å / SU ML: 0.3528 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.7179 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→44.5 Å
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Refine LS restraints |
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LS refinement shell |
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