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- PDB-1tkq: SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN IN A MEMBRA... -

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Entry
Database: PDB / ID: 1tkq
TitleSOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN IN A MEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE IN THE PRESENCE OF CsCl
Components
  • GRAMICIDIN A
  • MINI-GRAMICIDIN A
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologyMINI-GRAMICIDIN A - GRAMICIDIN A DIMER / SUCCINIC ACID / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsMINIMIZED AVERAGE
AuthorsXie, X. / Al-Momani, L. / Bockelmann, D. / Griesinger, C. / Koert, U.
Citation
Journal: FEBS J. / Year: 2005
Title: An Asymmetric Ion Channel Derived from Gramicidin A. Synthesis, Function and NMR Structure.
Authors: Xie, X. / Al-Momani, L. / Reiss, P. / Griesinger, C. / Koert, U.
#1: Journal: Science / Year: 1993
Title: High-Resolution Conformation of Gramicidin a in a Lipid Bilayer by Solid-State NMR
Authors: Ketchem, R.R. / Hu, W. / Cross, T.A.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Solution Structure of a Parallel Left-Handed Double-Helical Gramicidin-A Determined by 2D 1H NMR
Authors: Chen, Y. / Tucker, A. / Wallace, B.A.
#3: Journal: 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
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: 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 1.4Dec 12, 2012Group: Other
Revision 2.0Sep 25, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn ...atom_site / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _pdbx_nmr_spectrometer.model / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id
Revision 2.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MINI-GRAMICIDIN A
B: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4003
Polymers3,2822
Non-polymers1181
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area760 Å2
ΔGint6 kcal/mol
Surface area2810 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50MINIMIZED AVERAGE STRUCTURE OF 11 STRUCTURES WITH THE LOWEST TARGET FUNCTION
RepresentativeModel #1

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Components

#1: Protein/peptide MINI-GRAMICIDIN A


Type: Polypeptide / Class: Antibiotic / Mass: 1470.798 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE N-TERMINI OF THE TWO PEPTIDES, EACH A TRUNCATED GRAMICIDIN A, WERE LINKED BY A SUCCINIC ACID IN A HEAD-TO-HEAD MANNER.
Source: (synth.) BREVIBACILLUS BREVIS (bacteria)
References: NOR: NOR00243, MINI-GRAMICIDIN A - GRAMICIDIN A DIMER
#2: Protein/peptide GRAMICIDIN A / VALYL GRAMICIDIN


Type: Polypeptide / Class: Antibiotic / Mass: 1811.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE N-TERMINI OF THE TWO PEPTIDES, EACH A TRUNCATED GRAMICIDIN A, WERE LINKED BY A SUCCINIC ACID IN A HEAD-TO-HEAD MANNER.
Source: (synth.) BREVIBACILLUS BREVIS (bacteria)
References: NOR: NOR00243, MINI-GRAMICIDIN A - GRAMICIDIN A DIMER
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Type: Polypeptide / Class: Antibiotic / Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
Details: THE N-TERMINI OF THE TWO PEPTIDES, EACH A TRUNCATED GRAMICIDIN A, WERE LINKED BY A SUCCINIC ACID IN A HEAD-TO-HEAD MANNER.
References: MINI-GRAMICIDIN A - 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, MODIFIDED GRAMICIDIN A IS REPRESENTED BY TWO SEQUENCES (SEQRES AND ONE HET (SIN)
Has protein modificationN
Sequence detailsBOTH OF THE C-TERMINI HAVE ETHANOLAMINE ATTACHED WITH THE CAPPING GROUP T-BUTYLDIPHENYLSILYL, WHICH ...BOTH OF THE C-TERMINI HAVE ETHANOLAMINE ATTACHED WITH THE CAPPING GROUP T-BUTYLDIPHENYLSILYL, WHICH WAS APPLIED TO ENHANCE THE SOLUBILITY AND STABILITY OF THE STRUCTURE IN ORGANIC SOLVENTS. OWING TO AMBIGUITY IN RESONANCE ASSIGNMENT OF THE TERMINI AND THEREFORE A LACK OF ENOUGH NOE CONSTRAINTS, THE T-BUTYLDIPHENYLSILYL TERMINI WERE OMITTED IN THE STRUCTURE CALCULATION.

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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: VARIABLE TEMPERATURE EXPERIMENTS WERE PERFORMED TO HAVE THE TEMPERATURE DEPENDENCE OF NH CHEMICAL SHIFTS, THEREFORE PROVIDE EVIDENCE FOR HYDROGEN BONDING.

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Sample preparation

DetailsContents: 3MM SATURATED WITH CSCL
Sample conditionsTemperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SYBYL/DYANA 6.8GUENTERTrefinement
SYBYL/DYANA 6.8structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 160 NOE- DERIVED DISTANCE CONSTRAINTS, 39 DIHEDRAL ANGLE RESTRAINTS, AND 40 DISTANCE RESTRAINTS FROM HYDROGEN BONDS
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE STRUCTURE OF 11 STRUCTURES WITH THE LOWEST TARGET FUNCTION
Conformers calculated total number: 50 / Conformers submitted total number: 1

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