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- PDB-1mag: GRAMICIDIN A IN HYDRATED DMPC BILAYERS, SOLID STATE NMR -

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Entry
Database: PDB / ID: 1mag
TitleGRAMICIDIN A IN HYDRATED DMPC BILAYERS, SOLID STATE NMR
ComponentsGRAMICIDIN A
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN / ORIENTED BILAYERS
Function / homologyGRAMICIDIN A / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodSOLID-STATE NMR / simulated annealing
AuthorsKetchem, R.R. / Roux, B. / Cross, T.A.
Citation
Journal: J.Biomol.NMR / Year: 1996
Title: Macromolecular Structural Elucidation with Solid-State NMR-Derived Orientational Constraints.
Authors: Ketchem, R.R. / Lee, K.C. / Huo, S. / Cross, T.A.
#1: Journal: Biological Membranes: A Molecular Perspective from Computation and Experiment
Year: 1996
Title: Computational Refinement Through Solid State NMR and Energy Constraints of a Membrane Bound Polypeptide
Authors: Ketchem, R.R. / Roux, B. / Cross, T.A.
#2: Journal: Biochemistry / Year: 1995
Title: Lipid-Peptide Interface: Valine Conformation and Dynamics in the Gramicidin Channel
Authors: Lee, K.C. / Huo, S. / Cross, T.A.
#3: Journal: Biochemistry / Year: 1995
Title: Tryptophan Dynamics and Structural Refinement in a Lipid Bilayer Environment: Solid State NMR of the Gramicidin Channel
Authors: Hu, W. / Lazo, N.D. / Cross, T.A.
#4: 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.
History
DepositionJun 6, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: 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 1.5Dec 20, 2017Group: Database references / Other / Category: citation / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _pdbx_database_status.process_site
Revision 1.6Mar 14, 2018Group: Data collection / Derived calculations / Refinement description
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_refine / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_nmr_refine.details / _pdbx_nmr_refine.method ..._pdbx_nmr_refine.details / _pdbx_nmr_refine.method / _pdbx_nmr_software.authors / _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GRAMICIDIN A
B: GRAMICIDIN A


Theoretical massNumber of molelcules
Total (without water)3,7652
Polymers3,7652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area770 Å2
ΔGint-2 kcal/mol
Surface area2810 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide GRAMICIDIN A / VALYL GRAMICIDIN


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Source: (gene. exp.) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN A
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, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111SOLID STATE
121CROSS POLARIZED

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: CHEMAGNETICS CMX / Manufacturer: CHEMAGNETICS / Model: CMX / Field strength: 400 MHz

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Processing

NMR software
NameDeveloperClassification
TORCKETCHEM,ROUX,CROSSrefinement
TORCKETCHEM,ROUX,CROSSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: CHARMM23 STRUCTURE REFINED WITH TORC (TOTAL REFINEMENT OF CONSTRAINTS), DEVELOPED IN AUTHORS' LAB. TORC RUNS AS A MODULE WITHIN CHARMM AND UTILIZES A SIMULATED ANNEALING PROTOCOL TO REFINE ...Details: CHARMM23 STRUCTURE REFINED WITH TORC (TOTAL REFINEMENT OF CONSTRAINTS), DEVELOPED IN AUTHORS' LAB. TORC RUNS AS A MODULE WITHIN CHARMM AND UTILIZES A SIMULATED ANNEALING PROTOCOL TO REFINE THE STRUCTURE AGAINST BOTH THE SOLID STATE NMR DATA (INCLUDING SOLID STATE NMR DERIVED ORIENTATIONAL CONSTRAINTS) AND THE CHARMM ENERGY.
NMR ensembleConformers submitted total number: 1

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