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- PDB-1bdw: GRAMICIDIN D FROM BACILLUS BREVIS (ACTIVE FORM) -

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Basic information

Entry
Database: PDB / ID: 1bdw
TitleGRAMICIDIN D FROM BACILLUS BREVIS (ACTIVE FORM)
ComponentsGRAMICIDIN AGramicidin
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN / DOUBLE HELIX
Function / homologyGRAMICIDIN A / ACETIC ACID / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBurkhart, B.M. / Pangborn, W.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
DepositionMay 11, 1998Processing site: BNL
Revision 1.0Oct 14, 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 1.5Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0657
Polymers3,7652
Non-polymers3005
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-15 kcal/mol
Surface area2490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)20.584, 27.905, 52.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.996995, -0.076146, -0.014227), (-0.075848, 0.99691, -0.02042), (0.015738, -0.019279, -0.99969)
Vector: 10.31142, 0.42646, 7.99587)

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Components

#1: Protein/peptide GRAMICIDIN A / Gramicidin / VALYL GRAMICIDIN / Gramicidin


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 2 / 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-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / 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)

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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: 1.65 Å3/Da / Density % sol: 25.2 %
Crystal growpH: 2
Details: CRYSTALLIZED BY BATCH METHODS FROM A 30 MG/ML SOLUTION OF GRAMICIDIN D IN GLACIAL ACETIC ACID, PH 2.0, 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 RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1998 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 11715 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 28
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.125 / % possible all: 58.8
Reflection
*PLUS
Num. obs: 3416 / Num. measured all: 11715

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Processing

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

1av2


Resolution: 1.7→100 Å / Num. parameters: 1359 / Num. restraintsaints: 1360 / Cross valid method: FREE R / σ(F): 0 / StereochEM target val spec case: ETA BASED ON SERINE / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.243 159 5 %5% OF REFLECTIONS IN THIN RESOLUTION SHELLS.
all0.18 3416 --
obs0.168 -95 %-
Solvent computationSolvent model: MOEWS & KRETSINGER (G = 0.87873 U = 1.95930)
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 292 / Occupancy sum non hydrogen: 316
Refinement stepCycle: LAST / Resolution: 1.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms272 0 20 22 314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.237
X-RAY DIFFRACTIONs_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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