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Yorodumi- PDB-7jh6: De novo designed two-domain di-Zn(II) and porphyrin-binding protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jh6 | ||||||
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Title | De novo designed two-domain di-Zn(II) and porphyrin-binding protein | ||||||
Components | Two-domain di-Zn(II) and porphyrin-binding protein | ||||||
Keywords | DE NOVO PROTEIN / Metalloprotein / inter-domain coupling and cooperation / de novo protein design / allostery / synthetic porphyrin | ||||||
Function / homology | Chem-7BU Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Schmidt, N. / Liu, L. / DeGrado, W.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Allosteric cooperation in a de novo-designed two-domain protein. Authors: Pirro, F. / Schmidt, N. / Lincoff, J. / Widel, Z.X. / Polizzi, N.F. / Liu, L. / Therien, M.J. / Grabe, M. / Chino, M. / Lombardi, A. / DeGrado, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jh6.cif.gz | 315 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jh6.ent.gz | 261.5 KB | Display | PDB format |
PDBx/mmJSON format | 7jh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jh6_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7jh6_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7jh6_validation.xml.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/7jh6 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/7jh6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 4 - 177 / Label seq-ID: 1 - 174
NCS ensembles :
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-Components
#1: Protein | Mass: 20852.682 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-7BU / [ #4: Chemical | ChemComp-2PE / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 4000 100 mM MgCl2 100 mM Hepes pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→86.24 Å / Num. obs: 10708 / % possible obs: 99.63 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1552 / Rrim(I) all: 0.06219 / Net I/σ(I): 6.49 |
Reflection shell | Resolution: 3.5→3.625 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.184 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1008 / CC1/2: 0.322 / Rrim(I) all: 2.379 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Designed model Resolution: 3.5→86.24 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / 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 |
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Refinement step | Cycle: 1 / Resolution: 3.5→86.24 Å
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Refine LS restraints |
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