+Open data
-Basic information
Entry | Database: PDB / ID: 4z28 | ||||||
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Title | Crystal structure of short hoefavidin biotin complex | ||||||
Components | Avidin family | ||||||
Keywords | biotin-binding protein / high affinity system / bacterial avidins | ||||||
Function / homology | Function and homology information biotin binding / protein homodimerization activity / extracellular region Similarity search - Function | ||||||
Biological species | Hoeflea phototrophica DFL-43 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Livnah, O. / Avraham, O. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail. Authors: Avraham, O. / Meir, A. / Fish, A. / 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 | 4z28.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z28.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/4z28 ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z28 | HTTPS FTP |
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-Related structure data
Related structure data | 4z27SC 4z2oC 4z2pC 4z2vC 4z6jC 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: 14341.508 Da / Num. of mol.: 2 / Fragment: UNP residues 21-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hoeflea phototrophica DFL-43 (bacteria) Gene: HPDFL43_17171 / Production host: Escherichia coli (E. coli) / References: UniProt: A9D857 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Streak seeding was applied with source crystals. Crystals appeared within 24 hours and grew to their maximal size within 2 weeks |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. obs: 38372 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.66→1.72 Å / Rmerge(I) obs: 0.798 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z27 Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.661 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 33.531 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→50 Å
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Refine LS restraints |
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