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- PDB-1al4: GRAMICIDIN D FROM BACILLUS BREVIS (N-PROPANOL SOLVATE) -

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Basic information

Entry
Database: PDB / ID: 1al4
TitleGRAMICIDIN D FROM BACILLUS BREVIS (N-PROPANOL SOLVATE)
ComponentsGRAMICIDIN D
KeywordsANTIBIOTIC / ANTIFUNGAL / ANTIBACTERIAL / LINEAR GRAMICIDIN / MEMBRANE ION CHANNEL
Function / homologyGRAMICIDIN D / N-PROPANOL / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR PLACEMENT; DIFFERENCE MAPS / Resolution: 1.13 Å
AuthorsBurkhart, B.M. / Gassman, R.M. / Pangborn, W.A. / Duax, W.L.
CitationJournal: 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.
History
DepositionJun 11, 1997Processing site: BNL
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 1.5Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _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
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRAMICIDIN D
B: GRAMICIDIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,36612
Polymers3,7652
Non-polymers60110
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-5 kcal/mol
Surface area4840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.434, 32.461, 24.148
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: (0.84724, 0.15064, 0.5094), (0.15164, -0.98763, 0.03985), (0.5091, 0.04348, -0.85961)
Vector: -8.19, 65.16, 10.19)

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Components

#1: Protein/peptide GRAMICIDIN D


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) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN D
#2: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O
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: 1.69 Å3/Da / Density % sol: 27.15 % / Description: ISOMORPHOUS TO 1ALZ
Crystal growpH: 7
Details: CRYSTALLIZED BY BATCH METHODS FROM A SATURATED SOLUTION OF GRAMICIDIN D IN N-PROPANOL, PH 7.0, BATCH METHOD
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein11
32 %(w/v)PEG400011
2n-propanol11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.13→100 Å / Num. obs: 67561 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 47.6
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 13.7 / Rsym value: 0.065 / % possible all: 82.4
Reflection
*PLUS
Num. obs: 9572 / Num. measured all: 67561

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR PLACEMENT; DIFFERENCE MAPS
Starting model: PDB ENTRY 1ALZ

1alz


Resolution: 1.13→100 Å / Num. parameters: 3746 / Num. restraintsaints: 7423 / 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
Rfree0.121 563 5 %5% OF REFLECTIONS IN THIN RESOLUTION SHELLS.
all0.087 9571 --
obs0.085 -95.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER (G = 0.5373 U = 0.7755)
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 369.47 / Occupancy sum non hydrogen: 316.72
Refinement stepCycle: LAST / Resolution: 1.13→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms292 0 40 0 332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.411
X-RAY DIFFRACTIONs_zero_chiral_vol0.166
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.028
X-RAY DIFFRACTIONs_approx_iso_adps0.029
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.0851
Solvent computation
*PLUS
Displacement parameters
*PLUS

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