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Yorodumi- PDB-9bni: X-ray crystal structure of Cu-TZ4H-H3AH10D tryptophan zipper meta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bni | |||||||||
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Title | X-ray crystal structure of Cu-TZ4H-H3AH10D tryptophan zipper metallo-beta-sheet peptide | |||||||||
Components | Cu-TZ4H-H3AH10D tryptophan zipper metallo-beta-sheet peptide | |||||||||
Keywords | DE NOVO PROTEIN / beta-sheet | |||||||||
Function / homology | COPPER (II) ION Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 | 9bni.cif.gz | 24.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bni.ent.gz | 15.7 KB | Display | PDB format |
PDBx/mmJSON format | 9bni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bni_validation.pdf.gz | 610.2 KB | Display | wwPDB validaton report |
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Full document | 9bni_full_validation.pdf.gz | 610.2 KB | Display | |
Data in XML | 9bni_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 9bni_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/9bni ftp://data.pdbj.org/pub/pdb/validation_reports/bn/9bni | HTTPS FTP |
-Related structure data
Related structure data | 9bnhC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 1610.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 17 molecules
#2: Chemical | ChemComp-CL / | ||
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#3: Chemical | ChemComp-CU / | ||
#4: Chemical | ChemComp-P6G / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 M Ammonium Sulfate 0.1 M BIS-TRIS pH6.5 2% v/v PEG Monomethyl Ether 550 |
-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: Feb 15, 2023 |
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: 1.2→22.76 Å / Num. obs: 5049 / % possible obs: 99.98 % / Redundancy: 39.6 % / Biso Wilson estimate: 16.94 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 24.68 |
Reflection shell | Resolution: 1.2→1.243 Å / Num. unique obs: 492 / CC1/2: 0.781 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→22.76 Å / SU ML: 0.159 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.964 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: 29.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→22.76 Å
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Refine LS restraints |
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LS refinement shell |
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