+Open data
-Basic information
Entry | Database: PDB / ID: 1jjz | |||||||||
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Title | REFINED STRUCTURE AND DISULFIDE PAIRING OF THE KALATA B1 PEPTIDE | |||||||||
Components | Kalata-B4 | |||||||||
Keywords | PLANT PROTEIN / cyclic peptide / cyclotide / disulfide pairing / uterotonic | |||||||||
Function / homology | Function and homology information defense response / killing of cells of another organism / defense response to bacterium Similarity search - Function | |||||||||
Biological species | Oldenlandia affinis (plant) | |||||||||
Method | SOLUTION NMR / torsion angle dynamics | |||||||||
Authors | Skjeldal, L. / Gran, L. / Sletten, K. / Volkman, B.F. | |||||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2002 Title: Refined structure and metal binding site of the kalata B1 peptide. Authors: Skjeldal, L. / Gran, L. / Sletten, K. / Volkman, B.F. #1: Journal: Biochemistry / Year: 1995 Title: Elucidation of the Primary and Three-Dimensional Structure of the Uterotonic Polypeptide Kalata B1 Authors: Saether, O. / Craik, D.J. / Campbell, I.D. / Sletten, K. / Juul, J. / Norman, D.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jjz.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jjz.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jjz_validation.pdf.gz | 338.4 KB | Display | wwPDB validaton report |
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Full document | 1jjz_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 1jjz_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1jjz_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/1jjz ftp://data.pdbj.org/pub/pdb/validation_reports/jj/1jjz | HTTPS FTP |
-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 | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: Structure was determined using NOEs from a single 100 ms mixing time NOESY experiment |
-Sample preparation
Details | Contents: 5 mM kalata B1; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 0 / pH: 3 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: Structures are based on a total of 333 distance constraints. This includes 6 upper and 6 lower limits defining 3 disulfide bonds, as well as 3 upper and 3 lower limits defining a peptide ...Details: Structures are based on a total of 333 distance constraints. This includes 6 upper and 6 lower limits defining 3 disulfide bonds, as well as 3 upper and 3 lower limits defining a peptide bond cyclizing the peptide backbone. Residue numbering follows the original description of citation 1, except that for the purposes of structure calculations, the N-terminal residue was taken as Asn8. Therefore, residues 30-36 in this deposition correspond to residues 1-7 in citation 1 and related PDB entry 1kal. Structures were refined in the absence of any artificial constraints defining disulfide bonds until all NOEs had been assigned and low target functions were achieved (tf=0.6). 15 additional calculations were performed with these input data and the inclusion of constraints defining all possible disulfide pairing combinations. The structures containing disulfides between [5(34)-13], [17-29] and [22-27] displayed the lowest target function (0.74, second lowest was 1.54). On the basis of this result and analysis of NOEs observed between Cys sidechain protons, this disulfide bonding arrangement was assumed to be correct and served as the basis for this deposition. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20 |