+Open data
-Basic information
Entry | Database: PDB / ID: 7ouq | ||||||
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Title | wilavidin biotin complex | ||||||
Components | wilavidin | ||||||
Keywords | UNKNOWN FUNCTION / Biotin binding protein | ||||||
Function / homology | Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / biotin binding / extracellular region / BIOTIN / Avidin Function and homology information | ||||||
Biological species | Gammaproteobacteria bacterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Avraham, O. / Livnah, O. | ||||||
Citation | Journal: Febs J. / Year: 2022 Title: Wilavidin - a novel member of the avidin family that forms unique biotin-binding hexamers. Authors: Avraham, O. / Bayer, E.A. / Livnah, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ouq.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ouq.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ouq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ouq_validation.pdf.gz | 910.3 KB | Display | wwPDB validaton report |
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Full document | 7ouq_full_validation.pdf.gz | 915.7 KB | Display | |
Data in XML | 7ouq_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7ouq_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/7ouq ftp://data.pdbj.org/pub/pdb/validation_reports/ou/7ouq | HTTPS FTP |
-Related structure data
Related structure data | 7ourC 7p8yC 7p8zC 3szjS 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: 14047.544 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gammaproteobacteria bacterium (bacteria) Gene: C4528_07355 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A4VWA2 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | 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: 8.72 Å3/Da / Density % sol: 85.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976252 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976252 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→57.03 Å / Num. obs: 28877 / % possible obs: 99.8 % / Redundancy: 21.6 % / CC1/2: 0.999 / Rsym value: 0.149 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.63→2.77 Å / Num. unique obs: 2810 / CC1/2: 0.392 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SZJ Resolution: 2.63→57.03 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.065 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 244.71 Å2 / Biso mean: 73.486 Å2 / Biso min: 45.54 Å2
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Refinement step | Cycle: final / Resolution: 2.63→57.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.633→2.701 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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