+Open data
-Basic information
Entry | Database: PDB / ID: 6rei | ||||||
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Title | Crystal structure of Pizza6-S with Cd2+ | ||||||
Components | Pizza6-S | ||||||
Keywords | DE NOVO PROTEIN / Artificial beta-propeller protein / computational design / Cadmium / Pizza / Metalloprotein | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: To Be Published Title: Artificial beta-Propeller Protein-based Hydrolases Authors: Noguchi, H. / Clarke, D.E. / Gryspeerdt, J.L. / Feyter, S.D. / 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 | 6rei.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rei.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rei_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
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Full document | 6rei_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 6rei_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 6rei_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/6rei ftp://data.pdbj.org/pub/pdb/validation_reports/re/6rei | HTTPS FTP |
-Related structure data
Related structure data | 6relC 6remC 6reoC 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
#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-CD / #3: Chemical | ChemComp-CL / #4: Chemical | #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 | Density Matthews: 2.12 Å3/Da / Density % sol: 41.86 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / Details: 23%(w/v) PEG3350, 0.1M HEPES pH7.0, 30mM CdCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1808 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1808 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.73 Å / Num. obs: 69661 / % possible obs: 97.5 % / Redundancy: 22.2 % / Biso Wilson estimate: 9.15 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.037 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 11 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2829 / CC1/2: 0.903 / Rpim(I) all: 0.243 / % possible all: 83.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ww9 Resolution: 1.5→48.73 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→48.73 Å
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Refine LS restraints |
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LS refinement shell |
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