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Yorodumi- PDB-5wbb: Peroxide Activation Regulated by Hydrogen Bonds within Artificial... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wbb | ||||||
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Title | Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - S112A | ||||||
Components | Streptavidin | ||||||
Keywords | METAL BINDING PROTEIN / streptavidin / biotin / copper / hydroperoxo / secondary coordination sphere / hydrogen bond / biotin binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Mann, S.I. / Heinisch, T. / Ward, T.R. / Borovik, A.S. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins. Authors: Mann, S.I. / Heinisch, T. / Ward, T.R. / Borovik, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wbb.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wbb.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wbb_validation.pdf.gz | 995.7 KB | Display | wwPDB validaton report |
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Full document | 5wbb_full_validation.pdf.gz | 1001.2 KB | Display | |
Data in XML | 5wbb_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 5wbb_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/5wbb ftp://data.pdbj.org/pub/pdb/validation_reports/wb/5wbb | HTTPS FTP |
-Related structure data
Related structure data | 5wbaC 5wbdC 6anxC 2qcbS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16554.018 Da / Num. of mol.: 1 / Fragment: UNP residues 38-183 / Mutation: S112A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 |
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-Non-polymers , 5 types, 114 molecules
#2: Chemical | ChemComp-SQ1 / [ |
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#3: Chemical | ChemComp-CU / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-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: 46.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M sodium acetate, 2.6 M sodium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→55 Å / Num. obs: 25455 / % possible obs: 100 % / Redundancy: 9.6 % / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.5→1.53 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QCB Resolution: 1.5→55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.459 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.063 / 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: 19.241 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→55 Å
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Refine LS restraints |
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