+Open data
-Basic information
Entry | Database: PDB / ID: 1orl | ||||||
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Title | 1H NMR structure determination of Viscotoxin C1 | ||||||
Components | Viscotoxin C1 | ||||||
Keywords | TOXIN / helix-turn-helix / beta-sheet / concentric motif of disulphide bridges | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Viscum album (European mistletoe) | ||||||
Method | SOLUTION NMR / DYANA was employed for structure determination Discover was employed for energy minimisation of DYANA structures | ||||||
Authors | Molinari, H. / Romagnoli, S. / Fogolari, F. / Catalano, M. / Urech, K. / Giannattasio, M. / Ragona, L. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: NMR solution structure of viscotoxin C1 from Viscum album species Coloratum ohwi: toward a structure-function analysis of viscotoxins. Authors: Romagnoli, S. / Fogolari, F. / Catalano, M. / Zetta, L. / Schaller, G. / Urech, K. / Giannattasio, M. / Ragona, L. / Molinari, H. #1: Journal: Biochem.J. / Year: 2000 Title: NMR structural determination of viscotoxin A3 from Viscum album L. Authors: Molinari, H. / Romagnoli, S. / Fogolari, F. / Catalano, M. / Urech, K. / Giannattasio, M. / Ragona, L. | ||||||
History |
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Remark 999 | sequence The author indicated that the primary sequence for this protein has not yet been deposited ...sequence The author indicated that the primary sequence for this protein has not yet been deposited in any sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1orl.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1orl.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 1orl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1orl ftp://data.pdbj.org/pub/pdb/validation_reports/or/1orl | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 4954.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: viscotoxin C1 has been isolated from european mistletoe leaves Source: (natural) Viscum album (European mistletoe) / References: UniProt: P08943, UniProt: P83554*PLUS |
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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 1H 2D NMR techniques |
-Sample preparation
Details |
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Sample conditions |
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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 |
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-Processing
NMR software |
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Refinement | Method: DYANA was employed for structure determination Discover was employed for energy minimisation of DYANA structures Software ordinal: 1 Details: the structures are based on a total of 691 restraints. 631 are NOE-derived distance restraints,(224intraresidues,159 short range, 125 medium range and 123 long range), 18 dihedral angle ...Details: the structures are based on a total of 691 restraints. 631 are NOE-derived distance restraints,(224intraresidues,159 short range, 125 medium range and 123 long range), 18 dihedral angle restraints, 24 for backbone H-bonds and 18 for disulphide bridges. Bond lengths CD-OE2 in glutamic acid residues and CG-OD2 in aspartic acid residues are larger than typical values (as seen in remark 500) because protonated forms were considered due to the low experimental pH. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 600 / Conformers submitted total number: 10 |