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- PDB-1vm2: Solution structure of an anticancer peptide designed based on the... -

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Basic information

Entry
Database: PDB / ID: 1vm2
TitleSolution structure of an anticancer peptide designed based on the N-terminal sequence of E. coli enzyme IIA (Glucose)
Componentspeptide A2
KeywordsANTIBIOTIC / ANTIMICROBIAL PEPTIDE / BACTERIAL MEMBRANE ANCHOR / AMPHIPATHIC HELIX / ANTI-TUMOR PEPTIDE
MethodSOLUTION NMR / simulated annealing
AuthorsWang, G. / Li, X.
CitationJournal: 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
DepositionAug 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide A2


Theoretical massNumber of molelcules
Total (without water)1,4691
Polymers1,4691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 100No NOE violations greater than 0.50 A, 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
RepresentativeModel #1most resemble the average structure

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Components

#1: Protein/peptide peptide A2


Mass: 1468.717 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was synthesized using the solid-phase method and purified by HPLC.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY
131DQF-COSY
141ROESY
151(1H,15N)HSQC
161(1H,13C)HSQC
NMR detailsText: 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.

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Sample preparation

DetailsContents: 2mM peptide, 80mM sodium dodecylsulfate, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe/nmrDraw2.1Delaglio, F.data processing
PIPP1Garrett, D.noe picking
XPLOR-NIH1.06Schwieters, C.D., Kuszewski, J., Tjandra, N, Clore, G.M.refinement
MOLMOL2K.1Koradi, R.structural analysis and viewing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 124 distances derived from the NOESY spectra, 20 backbone dihedral angles derived from a set of chemical shifts using the NMR program TALOS, and 4 chi1 angle restraints.
NMR representativeSelection criteria: most resemble the average structure
NMR ensembleConformer selection criteria: No NOE violations greater than 0.50 A, 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 A, 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

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