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Yorodumi- PDB-1vm4: Solution structure of an antibacterial and antitumor peptide desi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vm4 | ||||||
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Title | Solution structure of an antibacterial and antitumor peptide designed based on the N-terminal membrane anchor of E. coli enzyme IIA (Glucose) | ||||||
Components | peptide A4 | ||||||
Keywords | ANTIBIOTIC / amphipathic helix / antimicrobial peptide / bacterial membrane anchor / anticancer peptide | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Wang, G. / Li, X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Correlation of Three-dimensional Structures with the Antibacterial Activity of a Group of Peptides Designed Based on a Nontoxic Bacterial Membrane Anchor. Authors: Wang, G. / Li, Y. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vm4.cif.gz | 26.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vm4.ent.gz | 17.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vm4_validation.pdf.gz | 342.9 KB | Display | wwPDB validaton report |
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Full document | 1vm4_full_validation.pdf.gz | 350.8 KB | Display | |
Data in XML | 1vm4_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 1vm4_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/1vm4 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/1vm4 | 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 | Mass: 1480.770 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was synthesized using the solid-phase method and purified by HPLC. The template sequence of the peptide is naturally found in Escherichia coli (bacteria). Source: (synth.) synthetic construct (others) |
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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 NMR techniques, plus the use of backbone angle restraints derived from a set of heteronuclear chemical shifts measured on the natural ...Text: This structure was determined using standard 2D homonuclear NMR techniques, plus the use of backbone angle restraints derived from a set of heteronuclear chemical shifts measured on the natural abundance peptide bound to micelles. |
-Sample preparation
Details | Contents: 2mM peptide, 80mM sodium dodecylsulfate, 90% H2O and 10% D2O Solvent system: 90% H2O and 10% D2O |
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Sample conditions | pH: 5.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on 109 distances derived from the NOESY spectra, 22 backbone dihedral angles derived from a set of chemical shifts using the NMR program TALOS, and 5 chi1 angle restraints. | ||||||||||||||||||||
NMR representative | Selection criteria: most resemble the average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: No NOE violations greater than 0.50, rms difference for bond deviations from ideality less than 0.01 A, rms difference for angle deviations from ideality less than 5 ...Conformer selection criteria: No NOE violations greater than 0.50, rms difference for bond deviations from ideality less than 0.01 A, rms difference for angle deviations from ideality less than 5 degrees, Structures with the lowerest energies in the ensemble. Conformers calculated total number: 100 / Conformers submitted total number: 5 |