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- PDB-1kqe: Solution structure of a linked shortened gramicidin A in benzene/... -

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Basic information

Entry
Database: PDB / ID: 1kqe
TitleSolution structure of a linked shortened gramicidin A in benzene/acetone 10:1
Components(MINI-GRAMICIDIN A) x 2
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN / METAL TRANSPORT
Function / homologyMINI-GRAMICIDIN A DIMER
Function and homology information
Biological speciesBrevibacillus brevis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsArndt, H.D. / Bockelmann, D. / Knoll, A. / Lamberth, S. / Griesinger, C. / Koert, U.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2002
Title: Cation Control in Functional Helical Programming: Structures of a D,L-Peptide Ion Channel
Authors: Arndt, H.D. / Bockelmann, D. / Knoll, A. / Lamberth, S. / Griesinger, C. / Koert, U.
History
DepositionJan 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Aug 10, 2011Group: Advisory
Revision 1.5Dec 12, 2012Group: Other
Revision 1.6Mar 6, 2013Group: Structure summary
Revision 1.7Mar 27, 2013Group: Database references
Revision 1.8Apr 10, 2013Group: Derived calculations
Revision 1.9Jul 18, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features / Item: _pdbx_molecule_features.details
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_site.pdbx_num_residues
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MINI-GRAMICIDIN A
B: MINI-GRAMICIDIN A
D: MINI-GRAMICIDIN A
E: MINI-GRAMICIDIN A


Theoretical massNumber of molelcules
Total (without water)6,2564
Polymers6,2564
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)1 / 200
Representativeclosest to the average

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Components

#1: Protein/peptide MINI-GRAMICIDIN A


Type: Polypeptide / Class: Antibiotic / Mass: 1613.939 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: GRAMICIDIN A RESIDUES 5-16, THE N-TERMINI OF THE TWO IDENTICAL PEPTIDES, EACH A TRUNCATED GRAMICIDIN A WERE LINKED BY A SUCCINIC ACID IN A HEAD-TO-HEAD MANNER.
Source: (synth.) Brevibacillus brevis (bacteria) / References: MINI-GRAMICIDIN A DIMER
#2: Protein/peptide MINI-GRAMICIDIN A


Type: Polypeptide / Class: Antibiotic / Mass: 1513.866 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: GRAMICIDIN A RESIDUES 5-16, THE N-TERMINI OF THE TWO IDENTICAL PEPTIDES, EACH A TRUNCATED GRAMICIDIN A WERE LINKED BY A SUCCINIC ACID IN A HEAD-TO-HEAD MANNER.
Source: (synth.) Brevibacillus brevis (bacteria) / References: MINI-GRAMICIDIN A DIMER
Compound detailsGRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D HERE, A MODIFIDED GRAMICIDIN A IS REPRESENTED BY TWO SEQUENCES (SEQRES) AND ONE HET (SIN)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
NMR detailsText: MINIMIZED AVERAGE STRUCTURE CALCULATED FROM THE SIXTEEN ENERGETICALLY FAVOURED STRUCTURES OUT OF THE TOTAL 200 CALCULATED STRUCTURES

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Sample preparation

Sample conditionsTemperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

Software
NameClassification
Felix2000data collection
X-PLORrefinement
FELIX2000data reduction
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 1

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