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

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Basic information

Entry
Database: PDB / ID: 1alz
TitleGRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
Components
  • ILE-GRAMICIDIN C
  • VAL-GRAMICIDIN A
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologyGRAMICIDIN A / GRAMICIDIN C / ETHANOL / : / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS, FOURIER RECYCLING / Resolution: 0.86 Å
AuthorsBurkhart, B.M. / Pangborn, W.A. / Duax, W.L. / Langs, D.A.
Citation
Journal: Biophys.J. / Year: 1998
Title: Heterodimer Formation and Crystal Nucleation of Gramicidin D
Authors: Burkhart, B.M. / Gassman, R.M. / Langs, D.A. / Pangborn, W.A. / Duax, W.L.
#1: Journal: Science / Year: 1988
Title: Three-Dimensional Structure at 0.86 A of the Uncomplexed Form of the Transmembrane Ion Channel Peptide Gramicidin A.
Authors: Langs, D.A.
History
DepositionJun 6, 1997Processing site: BNL
SupersessionMar 4, 1998ID: 1GMA
Revision 1.0Mar 4, 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 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ILE-GRAMICIDIN C
B: VAL-GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,40116
Polymers3,7562
Non-polymers64514
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-0 kcal/mol
Surface area5160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.595, 32.369, 24.219
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: (0.86723, 0.1584, 0.47203), (0.15867, -0.98654, 0.03955), (0.47194, 0.0406, -0.88069)
Vector: -8.48, 64.92, 11.57)

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Components

#1: Protein/peptide ILE-GRAMICIDIN C


Type: Polypeptide / Class: Antibiotic / Mass: 1873.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: GRAMICIDIN C 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: NOR00248, GRAMICIDIN C
#2: Protein/peptide VAL-GRAMICIDIN A


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 1 / 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
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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 AND C ARE REPRESENTED BY THE SEQUENCE (SEQRES)
Sequence detailsTHE SEQUENCE IS FOR THE MAJOR COMPONENT GRAMICIDIN C (QIL1 AND TRP11) WHILE THE MINOR COMPONENT ...THE SEQUENCE IS FOR THE MAJOR COMPONENT GRAMICIDIN C (QIL1 AND TRP11) WHILE THE MINOR COMPONENT (FVA1 AND TYR11) IS REPRESENTED IN SEQADV WITH MICROHETEROGENEITY. NOTE: QIL1 AND FVA1 ARE FORMYLATED ILE1 AND VAL1, RESPECTIVELY.

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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: 1.76 Å3/Da / Density % sol: 30 %
Crystal growpH: 7
Details: CRYSTALLIZED BY BATCH METHODS FROM A SATURATED SOLUTION OF GRAMICIDIN D IN ETHANOL., PH 7.0, BATCH METHOD
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein11
22 %(w/v)PEG400011
3n-propanol11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1987 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.86→100 Å / Num. obs: 21454 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 1.1 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 5.1
Reflection shellResolution: 0.86→0.9 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.043 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.043 / % possible all: 93.6
Reflection
*PLUS
Rmerge(I) obs: 0.1641

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
SIEMENSdata reduction
SIEMENSdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: DIRECT METHODS, FOURIER RECYCLING
Resolution: 0.86→100 Å / Num. parameters: 3464 / Num. restraintsaints: 5742 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: MODIFIED ENGH AND HUBER FOR ETHANOLAMINE BASED ON SERINE
Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1033 5 %5% OF REFLECTIONS IN THIN RESOLUTION SHELLS.
all0.162 21454 --
obs0.162 -99.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER (G = 0.22140 U = 1.29472)
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 365.06 / Occupancy sum non hydrogen: 312.16
Refinement stepCycle: LAST / Resolution: 0.86→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms294 0 42 1 337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.339
X-RAY DIFFRACTIONs_zero_chiral_vol0.114
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.113
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.036
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1618
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.339
X-RAY DIFFRACTIONs_chiral_restr0.114

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