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- PDB-1gmk: GRAMICIDIN/KSCN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1gmk
TitleGRAMICIDIN/KSCN COMPLEX
ComponentsGRAMICIDIN A
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN / DOUBLE HELIX
Function / homologyGRAMICIDIN A / : / METHANOL / THIOCYANATE ION / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDoyle, D.A. / Wallace, B.A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal Structure of the Gramicidin/Potassium Thiocyanate Complex.
Authors: Doyle, D.A. / Wallace, B.A.
#1: Journal: Biophys.J. / Year: 1994
Title: The Structure of the Gramicidin/Kscn Complex
Authors: Doyle, D.A. / Wallace, B.A.
#2: Journal: Ann.N.Y.Acad.Sci. / Year: 1984
Title: Crystalline Ion Complexes of Gramicidin A
Authors: Kimball, M.R. / Wallace, B.A.
History
DepositionJul 9, 1996Processing site: BNL
Revision 1.0Jul 1, 1998Provider: 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 1.5Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: GRAMICIDIN A
D: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,71937
Polymers7,5294
Non-polymers1,19033
Water00
1
C: GRAMICIDIN A
D: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,34919
Polymers3,7652
Non-polymers58517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-25.2 kcal/mol
Surface area4010 Å2
MethodPISA
2
A: GRAMICIDIN A
B: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,36918
Polymers3,7652
Non-polymers60516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-26.3 kcal/mol
Surface area4040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.060, 51.800, 31.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
GRAMICIDIN A / VALYL GRAMICIDIN


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 4 / Source method: isolated from a natural 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: (natural) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN A
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#4: Chemical...
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: CH4O
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)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDescription: DATA COLLECTED AT ROOM TEMPERATURE WITH CRYSTAL IN METHANOL.
Crystal growDetails: CRYSTALLIZED IN METHANOL
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein11
373.3 mMpotassium thiocyanate11
2methanol11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 11, 1991
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 5476 / % possible obs: 73.3 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.0325

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
CADRALdata reduction
SHELX76data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GRAMICIDIN/CSCL COMPLEX, THEN GRAMICIDIN/CSSCN COMPLEX, BOTH WITHOUT IONS

Resolution: 2.5→10 Å / σ(F): 3
Details: THE LOW TEMPERATURE FACTORS OF ATOMS N OF SCN 1, 2, 3, AND 4 ARE PROBABLY DUE TO POSITIONAL DISORDER OF THE THIOCYANATE MOLECULE WITH THE RESULT THAT OCCASIONALLY THE HEAVY SULFUR ATOM IS ...Details: THE LOW TEMPERATURE FACTORS OF ATOMS N OF SCN 1, 2, 3, AND 4 ARE PROBABLY DUE TO POSITIONAL DISORDER OF THE THIOCYANATE MOLECULE WITH THE RESULT THAT OCCASIONALLY THE HEAVY SULFUR ATOM IS SITUATED CLOSE TO THE PRESENT LOCATION OF THE NITROGEN. TWO METHANOL MOLECULES, MOH 5 AND MOH 19, WERE PLACED IN DENSITIES THAT ARE BELIEVED TO BELONG TO COMBINED DISORDERED CONFORMATIONS OF TRP A 15 AND TRP C 9 (MOH 19), AND TRP D 15 AND TRP A 9 (MOH 5).
RfactorNum. reflection% reflection
Rwork0.192 --
obs0.192 2241 83.3 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms517 0 66 0 583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.78
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.14
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.147
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.567

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