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- PDB-1av2: Gramicidin A/CsCl complex, active as a dimer -

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Basic information

Entry
Database: PDB / ID: 1av2
TitleGramicidin A/CsCl complex, active as a dimer
ComponentsGRAMICIDIN A
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologyGRAMICIDIN A / : / METHANOL / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT/ ANOMALOUS SCATTERING / Resolution: 1.4 Å
AuthorsBurkhart, B.M. / Li, N. / Langs, D.A. / Duax, W.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: The Conducting Form of Gramicidin a is a Right-Handed Double-Stranded Double Helix.
Authors: Burkhart, B.M. / Li, N. / Langs, D.A. / Pangborn, W.A. / Duax, W.L.
History
DepositionSep 23, 1997Processing 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 1.5Feb 6, 2013Group: Derived calculations
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.pdbx_ptnr2_label_alt_id / _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 / _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 2.2Nov 13, 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

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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)8,89024
Polymers7,5294
Non-polymers1,36120
Water39622
1
A: GRAMICIDIN A
B: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,62316
Polymers3,7652
Non-polymers85914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-372 kcal/mol
Surface area5120 Å2
2
C: GRAMICIDIN A
D: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2668
Polymers3,7652
Non-polymers5026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.060, 31.880, 52.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.87519, 0.48351, -0.01586), (0.48374, 0.87433, -0.0392), (-0.00509, -0.04198, -0.99911)36.49, -8.05, 67.49
2given(-0.89416, 0.44768, 0.00763), (0.44774, 0.89412, 0.00918), (-0.00271, 0.01162, -0.99993)43.94, -10.75, 64.58
3given(-0.99977, -0.02099, 0.00381), (0.02104, -0.99968, 0.01396), (0.00352, 0.01404, 0.9999)46.49, 14.96, 1.03

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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-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cs
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 30 %
Crystal growpH: 7
Details: 30 MG/ML GRAMICIDIN, SATURATED CSCL, METHANOL, PH 7.0, BATCH METHOD
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlmethanolic solution11
2250 mM11CsCl

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 15, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 108451 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 59
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.152 / % possible all: 54.5
Reflection
*PLUS
Num. obs: 17776 / % possible obs: 91.3 % / Num. measured all: 39976 / Rmerge(I) obs: 0.055

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT/ ANOMALOUS SCATTERING
Starting model: HOME-MADE MODEL

Resolution: 1.4→100 Å / Num. parameters: 5261 / Num. restraintsaints: 6720 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
Details: METHANOL MOLECULES WERE KEPT ISOTROPIC WITH NO HYDROGENS BECAUSE OF HIGH DISORDER. THE BIJVOET DIFFERENCES WERE USED IN PHASING
RfactorNum. reflection% reflection
Rfree0.186 1788 5 %
all0.156 17776 -
obs0.154 -92.4 %
Solvent computationSolvent model: MOEWS & KRETSINGER (G = 0.83086, U = 1.41203)
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 560 / Occupancy sum non hydrogen: 572.47
Refinement stepCycle: LAST / Resolution: 1.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms544 0 29 22 595
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.311
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS

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