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Yorodumi- PDB-4z2o: High resolution crystal structure of short hoefavidin-hoef-peptid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z2o | ||||||
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Title | High resolution crystal structure of short hoefavidin-hoef-peptide complex | ||||||
Components |
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Keywords | biotin binding protein / protein binding / high affinity system / bacterial avidins / biotin | ||||||
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: 1.17 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 | 4z2o.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z2o.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 4z2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z2o_validation.pdf.gz | 413.9 KB | Display | wwPDB validaton report |
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Full document | 4z2o_full_validation.pdf.gz | 414 KB | Display | |
Data in XML | 4z2o_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 4z2o_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/4z2o ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z2o | HTTPS FTP |
-Related structure data
Related structure data | 4z27SC 4z28C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14341.508 Da / Num. of mol.: 1 / 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 |
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#2: Protein/peptide | Mass: 1235.339 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hoeflea phototrophica DFL-43 (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A9D857*PLUS |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M NaCl, 0.1 M Bis-Tris pH 6.2-7.0 and 1.1-1.5 M ammonium sulfate PH range: 6.2-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→50 Å / Num. obs: 39465 / % possible obs: 99 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.17→1.21 Å / Rmerge(I) obs: 0.602 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z27 Resolution: 1.17→38.96 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.156 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035 / 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: 14.377 Å2
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Refinement step | Cycle: 1 / Resolution: 1.17→38.96 Å
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Refine LS restraints |
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