+Open data
-Basic information
Entry | Database: PDB / ID: 6reh | ||||||
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Title | Crystal structure of Pizza6-S with Cu2+ | ||||||
Components | Pizza6-S | ||||||
Keywords | DE NOVO PROTEIN / Artificial beta-propeller protein / computational design / Copper / Pizza / Metalloprotein | ||||||
Function / homology | TolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / COPPER (II) ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Noguchi, H. / Clarke, D.E. / Gryspeerdt, J.L. / Feyter, S.D. / Voet, A.R.D. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 Title: Artificial beta-propeller protein-based hydrolases. Authors: Clarke, D.E. / Noguchi, H. / Gryspeerdt, J.A.G. / De Feyter, S. / Voet, A.R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6reh.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6reh.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 6reh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6reh_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 6reh_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 6reh_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 6reh_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/6reh ftp://data.pdbj.org/pub/pdb/validation_reports/re/6reh | HTTPS FTP |
-Related structure data
Related structure data | 6regC 6rejC 6rekC 6renC 3ww9S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25719.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: 0.2M Ammonium sulfate, 0.1M Sodium acetate, 22%(w/v) PEG4000, 20mM CuCl2 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97875 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97875 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→24.72 Å / Num. obs: 37168 / % possible obs: 97.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 23.48 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.048 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2019 / CC1/2: 0.785 / Rpim(I) all: 0.457 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ww9 Resolution: 1.73→24.025 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→24.025 Å
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Refine LS restraints |
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LS refinement shell |
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