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Yorodumi- PDB-5wll: De Novo Design of Polynuclear Transition Metal Clusters in Helix ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wll | ||||||
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Title | De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 | ||||||
Components | Helical Bundle 4DH1 | ||||||
Keywords | DE NOVO PROTEIN / Protein Design / Helical Bundle / Metal Binding | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zhang, S.-Q. / Liu, L. / DeGrado, W.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles. Authors: Zhang, S.Q. / Chino, M. / Liu, L. / Tang, Y. / Hu, X. / DeGrado, W.F. / Lombardi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wll.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wll.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 5wll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wll_validation.pdf.gz | 396.3 KB | Display | wwPDB validaton report |
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Full document | 5wll_full_validation.pdf.gz | 396.3 KB | Display | |
Data in XML | 5wll_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 5wll_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/5wll ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wll | HTTPS FTP |
-Related 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/peptide | Mass: 3205.660 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 4.81 Å3/Da / Density % sol: 74.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0% PEG1000, 1.0 M AmSO4 and 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2015 |
Radiation | Monochromator: Double-Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→70.01 Å / Num. obs: 19614 / % possible obs: 99.2 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 10 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3086 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→70.01 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.953 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / 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: 25.171 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→70.01 Å
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Refine LS restraints |
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