+Open data
-Basic information
Entry | Database: PDB / ID: 6xnd | ||||||
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Title | Avidin-Biotin-Phenol | ||||||
Components | Avidin | ||||||
Keywords | STRUCTURAL PROTEIN / the complex of Avidin and Biotin-Phenol / Structural Genomics / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Ahmadvand, P. / Kang, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chemmedchem / Year: 2020 Title: A Ligand-Directed Nitrophenol Carbonate for Transient in situ Bioconjugation and Drug Delivery Authors: Burt, A.J. / Ahmadvand, P. / Opp, L.K. / Ryan, A.T. / Kang, C. / Mancini, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xnd.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xnd.ent.gz | 155.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xnd_validation.pdf.gz | 828.6 KB | Display | wwPDB validaton report |
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Full document | 6xnd_full_validation.pdf.gz | 852.2 KB | Display | |
Data in XML | 6xnd_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 6xnd_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/6xnd ftp://data.pdbj.org/pub/pdb/validation_reports/xn/6xnd | HTTPS FTP |
-Related structure data
Related structure data | 2aviS 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: 14350.081 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVD / Production host: Gallus gallus (chicken) / References: UniProt: P02701 #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-V8M / 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: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris, pH 7.0, and 25% (w/v) PEG 1500 / PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→44.843 Å / Num. obs: 71463 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 10.23 |
Reflection shell | Resolution: 1.58→1.64 Å / Num. unique obs: 6991 / CC1/2: 0.462 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AVI Resolution: 1.58→44.843 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.63 Å2 / Biso mean: 34.3868 Å2 / Biso min: 15.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→44.843 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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