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Yorodumi- PDB-1ed0: NMR structural determination of viscotoxin A3 from Viscum album L. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ed0 | ||||||
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Title | NMR structural determination of viscotoxin A3 from Viscum album L. | ||||||
Components | VISCOTOXIN A3 | ||||||
Keywords | TOXIN / THIONIN / CONCENTRIC MOTIF / HELIX-TURN-HELIX / ALPHA-BETA PROTEIN / AMPHIPATHIC HELIX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Viscum album (European mistletoe) | ||||||
Method | SOLUTION NMR / RESTRAINED SIMULATED ANNEALING IN TORSION ANGLE SPACE, ITERATIVE RESTRAINTS REFINEMENT, RESTRAINED MOLECULAR DYNAMICS IN CARTESIAN COORDINATE SPACE MINIMIZATION | ||||||
Authors | Romagnoli, S. / Ugolini, R. / Fogolari, F. / Schaller, G. / Urech, K. / Giannattasio, M. / Ragona, L. / Molinari, H. | ||||||
Citation | Journal: Biochem.J. / Year: 2000 Title: NMR structural determination of viscotoxin A3 from Viscum album L. Authors: Romagnoli, S. / Ugolini, R. / Fogolari, F. / Schaller, G. / Urech, K. / Giannattasio, M. / Ragona, L. / Molinari, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ed0.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ed0.ent.gz | 114.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ed0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ed0_validation.pdf.gz | 326.8 KB | Display | wwPDB validaton report |
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Full document | 1ed0_full_validation.pdf.gz | 359.2 KB | Display | |
Data in XML | 1ed0_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1ed0_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/1ed0 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/1ed0 | HTTPS FTP |
-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: 4842.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P01538 |
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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 |
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Sample conditions | Ionic strength: 50mM / pH: 3.6 / Pressure: ambient / Temperature: 285 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: RESTRAINED SIMULATED ANNEALING IN TORSION ANGLE SPACE, ITERATIVE RESTRAINTS REFINEMENT, RESTRAINED MOLECULAR DYNAMICS IN CARTESIAN COORDINATE SPACE MINIMIZATION Software ordinal: 1 Details: 1010 distance restraints were calculated reduced to 734 (230 intraresidue, 172 sequential, 191 medium range, 141 long range) after removal of irrelevant restraints. Calculation started with ...Details: 1010 distance restraints were calculated reduced to 734 (230 intraresidue, 172 sequential, 191 medium range, 141 long range) after removal of irrelevant restraints. Calculation started with 200 randomized conformers and consistently violated restraints were checked and relaxed where necessary. This procedure was repeated until no consistent violations were found in half or more of the structures. 600 new calculations were started and the 20 structures with lowest target function were analyzed. The structure with lowest target function and the structure exhibiting the largest RMSD with it were subjected to restrained molecular dynamics (20 cycles of 15 ps restrained molecular dynamics followed by minimization). All even structures from the last 10 minimized structures were retained from both sets and deposited. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest average rmsd with other structures in the ensemble | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 10 |