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- PDB-3l8l: Gramicidin D complex with sodium iodide -

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Basic information

Entry
Database: PDB / ID: 3l8l
TitleGramicidin D complex with sodium iodide
Components(GRAMICIDIN D) x 2
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN / GRAMICIDIN-NAI COMPLEX
Function / homologyGRAMICIDIN D / IODIDE ION / METHANOL / :
Function and homology information
Biological speciesBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsOlczak, A. / Glowka, M.L. / Szczesio, M. / Bojarska, J. / Wawrzak, Z. / Duax, W.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex.
Authors: Olczak, A. / Glowka, M.L. / Szczesio, M. / Bojarska, J. / Wawrzak, Z. / Duax, W.L.
History
DepositionDec 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: 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 1.4Mar 28, 2012Group: Database references
Revision 1.5Dec 12, 2012Group: Other
Revision 1.6Feb 13, 2013Group: Derived calculations
Revision 1.7Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_ptnr1_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _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 D
B: GRAMICIDIN D
C: GRAMICIDIN D
D: GRAMICIDIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,52818
Polymers7,4514
Non-polymers1,07614
Water75742
1
A: GRAMICIDIN D
B: GRAMICIDIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,37511
Polymers3,7262
Non-polymers6509
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area2930 Å2
MethodPISA
2
C: GRAMICIDIN D
D: GRAMICIDIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1527
Polymers3,7262
Non-polymers4275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-12 kcal/mol
Surface area2900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.816, 31.255, 51.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide GRAMICIDIN D / VAL-GRAMICIDIN A


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GRAMICIDIN D IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 1). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Source: (natural) BACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN D
#2: Protein/peptide GRAMICIDIN D / VAL-GRAMICIDIN A


Type: Polypeptide / Class: Antibiotic / Mass: 1843.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GRAMICIDIN D IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 1). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Source: (natural) BACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN D

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Non-polymers , 4 types, 56 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

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 D IS REPRESENTED BY THE SEQUENCE (SEQRES)

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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: 1.61 Å3/Da / Density % sol: 23.72 %
Crystal growDetails: BATCH CRYSTALLIZATION WITH 30 MG/ML GRAMICIDIN AND SATURATED NAI IN METHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.918
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.25→26.74 Å / Num. obs: 19883 / Observed criterion σ(I): 2

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W5U

1w5u


Resolution: 1.25→26.74 Å / Num. parameters: 5345 / Num. restraintsaints: 6738 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
all0.164 24628 --
obs--100 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 26 / Occupancy sum hydrogen: 556.13 / Occupancy sum non hydrogen: 566.51
Refinement stepCycle: LAST / Resolution: 1.25→26.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms566 0 17 42 625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.033
X-RAY DIFFRACTIONs_zero_chiral_vol0.146
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.126
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0

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