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Yorodumi- PDB-1jy4: B4DIMER: A DE NOVO DESIGNED EIGHT-STRANDED BETA-SHEET ASSEMBLED U... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jy4 | ||||||
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Title | B4DIMER: A DE NOVO DESIGNED EIGHT-STRANDED BETA-SHEET ASSEMBLED USING A DISULFIDE BOND | ||||||
Components | B4DIMER | ||||||
Keywords | DE NOVO PROTEIN / eight-stranded beta-sheet / disulfide bond / de novo protein design | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Authors | Venkatraman, J. / Nagana Gowda, G.A. / Balaram, P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2002 Title: Design and construction of an open multistranded beta-sheet polypeptide stabilized by a disulfide bridge. Authors: Venkatraman, J. / Nagana Gowda, G.A. / Balaram, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jy4.cif.gz | 208 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jy4.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jy4 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jy4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3937.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
-Sample preparation
Details | Contents: 1mM B4dimer, CD3OH / Solvent system: CD3OH |
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Sample conditions | Ionic strength: unbuffered / Pressure: ambient / Temperature: 300 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 Details: The ten structures were determined by NMR and torsion angle dynamics/simulated annealing methods. The peptide dimer was treated as a single entity and symmetry elements were not utilized ...Details: The ten structures were determined by NMR and torsion angle dynamics/simulated annealing methods. The peptide dimer was treated as a single entity and symmetry elements were not utilized during structure calculations. The structures are based on a total of 446 restraints, 398 are NOE-derived distance constraints,48 distance restraints are from hydrogen bonds. The list of constraints is available in the file dyana_upperconst.txt. Structure calculations were performed with the program DYANA-1.5 (P. Guentert, C. Mumenthaler, K. Wuthrich, J. Mol. Biol.(1997)Vol.273, 283-298). No violation of distance constraints from NOEs exceeded 0.3Angstroms. The ensemble of structures is superimposed over the best-structured region encompasing residues E11-L34. The average RMSDs between the superposed structures and the average structure are as follows: 0.75(chain A, residues 11-34, backbone atoms) 0.72(chain B, residues 11-34, backbone atoms. | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |