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Yorodumi- PDB-9bnh: X-ray Crystal Structure of Cu-TZ4H tryptophan Zipper Metallo-Peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bnh | ||||||
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Title | X-ray Crystal Structure of Cu-TZ4H tryptophan Zipper Metallo-Peptide | ||||||
Components | Cu-TZ4H tryptophan Zipper Metallo-Peptide | ||||||
Keywords | DE NOVO PROTEIN / copper / beta-sheet / hairpin | ||||||
Function / homology | ACETIC ACID / COPPER (II) ION / AMMONIA / TRIETHYLENE GLYCOL Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Dang, V.T. / Nguyen, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chemistry / Year: 2024 Title: Crystallography reveals metal-triggered restructuring of beta-hairpins. Authors: Dang, V.T. / Engineer, A. / McElheny, D. / Drena, A. / Telser, J. / Tomczak, K. / Nguyen, A.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bnh.cif.gz | 36 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bnh.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 9bnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bnh_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 9bnh_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 9bnh_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 9bnh_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/9bnh ftp://data.pdbj.org/pub/pdb/validation_reports/bn/9bnh | HTTPS FTP |
-Related structure data
Related structure data | 9bniC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein/peptide , 1 types, 2 molecules AB
#1: Protein/peptide | Mass: 1702.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 6 types, 51 molecules
#2: Chemical | #3: Chemical | ChemComp-ACY / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.46 Å3/Da / Density % sol: 50 % Description: Cubic translucent crystals with light purple coloring |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Crystal Grown: 6.0 M Ammonium Nitrate, 0.1 M Sodium Acetate Trihydrate pH 4.6 (pH adjusted with HCl) Cryo-protection: 10% v/v PEG 400 (soaked) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2022 |
Radiation | Monochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→19.41 Å / Num. obs: 12507 / % possible obs: 97.98 % / Redundancy: 6.4 % / Biso Wilson estimate: 9.27 Å2 / CC1/2: 0.969 / CC star: 0.981 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.12→1.16 Å / Num. unique obs: 964 / CC1/2: 0.963 / CC star: 0.991 / % possible all: 94.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→16.48 Å / SU ML: 0.0731 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.3975 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→16.48 Å
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Refine LS restraints |
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LS refinement shell |
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