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- PDB-1w5u: GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE) -

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Basic information

Entry
Database: PDB / ID: 1w5u
TitleGRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
ComponentsGRAMICIDIN DGramicidin
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologyGRAMICIDIN D / ETHANOL / RUBIDIUM ION
Function and homology information
Biological speciesBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsGlowka, M.L. / Olczak, A. / Bojarska, J. / Szczesio, M. / Duax, W.L. / Burkhart, B.M. / Pangborn, W.A. / Langs, D.A. / Wawrzak, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Gramicidin D-Rbcl Complex at Atomic Resolution from Low-Temperature Synchrotron Data: Interactions of Double-Stranded Gramicidin Channel Contents and Cations with Channel Wall
Authors: Glowka, M.L. / Olczak, A. / Bojarska, J. / Szczesio, M. / Duax, W.L. / Burkhart, B.M. / Pangborn, W.A. / Langs, D.A. / Wawrzak, Z.
History
DepositionAug 10, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
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.status_code_sf / _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.ptnr2_auth_asym_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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)8,98525
Polymers7,5294
Non-polymers1,45521
Water55831
1
A: GRAMICIDIN D
B: GRAMICIDIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,36912
Polymers3,7652
Non-polymers60510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-34.7 kcal/mol
Surface area3360 Å2
MethodPQS
2
C: GRAMICIDIN D
D: GRAMICIDIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,61513
Polymers3,7652
Non-polymers85111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-30.8 kcal/mol
Surface area3580 Å2
MethodPQS
Unit cell
Length a, b, c (Å)30.060, 31.300, 51.691
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 D / Gramicidin / VAL-GRAMICIDIN A / Gramicidin


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 4 / 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: GRAMICIDIN D
#2: Chemical
ChemComp-RB / RUBIDIUM ION / VAL-GRAMICIDIN A / Rubidium


Mass: 85.468 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Rb / Source: (natural) BACILLUS BREVIS (bacteria)
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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 COLLECTIVELY CALLED GRAMICIDIN D HERE, GRAMICIDIN D IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: GRAMICIDIN A CHAIN: A, C COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 16 DESCRIPTION: 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). RESPECTIVELY. GROUP: 2 NAME: GRAMICIDIN A CHAIN: B, D COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 16 DESCRIPTION: 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). THE DBREF FOR EACH CHAIN IS FOR THE MAJOR COMPONENT OF GRAMICIDIN A (TRP11), WHILE THE MINOR COMPONENTS (PHE11) IS REPRESENTED BY SEQADV WITH MICROHETEROGENEITY

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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: 23.83 %
Crystal growDetails: BATCH CRYSTALLIZATION WITH 30 MG/ML GRAMICIDIN AND SATURATED RBCL IN ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.71
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.14→20 Å / Num. obs: 33140 / % possible obs: 98.7 % / Redundancy: 8.25 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.5
Reflection shellResolution: 1.14→20 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.4 / % possible all: 97.2

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AV2

1av2


Resolution: 1.14→20 Å / Num. parameters: 6591 / Num. restraintsaints: 9395 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1628 5 %RANDOM
all0.1731 33140 --
obs0.1714 -98.7 %-
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 557.77 / Occupancy sum non hydrogen: 570.12
Refinement stepCycle: LAST / Resolution: 1.14→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 23 31 621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.138
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0

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