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- PDB-2xdc: Structure of linear gramicidin D obtained using Type I crystals g... -

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Entry
Database: PDB / ID: 2xdc
TitleStructure of linear gramicidin D obtained using Type I crystals grown in a lipid cubic phase.
ComponentsGRAMICIDIN A
KeywordsANTIBIOTIC / ION CHANNEL / MONOOLEIN / LIPID CUBIC PHASE / MESOPHASE SPONGE PHASE / BILAYER / ANTIFUNGAL / ANTIBACTERIAL
Function / homologyGRAMICIDIN A / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHoefer, N. / Aragao, D. / Caffrey, M.
CitationJournal: Biophys.J. / Year: 2010
Title: Crystallizing Transmembrane Peptides in Lipidic Mesophases
Authors: Hoefer, N. / Aragao, D. / Caffrey, M.
History
DepositionApr 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: 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 1.2Aug 29, 2012Group: Database references / Refinement description
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Mar 29, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRAMICIDIN A
B: GRAMICIDIN A
C: GRAMICIDIN A
D: GRAMICIDIN A
E: GRAMICIDIN A
F: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,43611
Polymers11,2946
Non-polymers6,1425
Water362
1
A: GRAMICIDIN A
B: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3776
Polymers3,7652
Non-polymers4,6124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-19 kcal/mol
Surface area4080 Å2
MethodPISA
2
E: GRAMICIDIN A
F: GRAMICIDIN A


Theoretical massNumber of molelcules
Total (without water)3,7652
Polymers3,7652
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-14.2 kcal/mol
Surface area3020 Å2
MethodPISA
3
C: GRAMICIDIN A
D: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2943
Polymers3,7652
Non-polymers1,5301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-13 kcal/mol
Surface area3110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.500, 62.560, 30.530
Angle α, β, γ (deg.)90.00, 99.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.05981, -0.03119, -0.99772), (-0.15034, -0.98839, 0.02189), (-0.98682, 0.14869, -0.06381)33.76385, -4.49545, 16.96919
2given(-0.98083, 0.15254, 0.12125), (0.15147, 0.9883, -0.01811), (-0.12259, 0.00061, -0.99246)-1.96999, 0.70732, 21.14136

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Components

#1: Protein/peptide
GRAMICIDIN A / VALYL GRAMICIDIN


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 6 / 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-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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 A IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: GRAMICIDIN A CHAIN: A, B, C ,D, E, F COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 16 DESCRIPTION: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM VALINE IS FORMYLATED (RESIDUE 1). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51 %
Description: DATA WERE COLLECTED USING A COLLIMATED MINIBEAM WITH A 10 MICRON BEAMSIZE.
Crystal growMethod: lipidic cubic phase / pH: 9
Details: 20 %(W/V) POLYETHYLENE GLYCOL (PEG) 6000, 0.1 M BICINE, PH 9.0. LIPIDIC CUBIC PHASE OF MONOOLEIN WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO MONOOLEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03312
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 16, 2008 / Details: SI(111) DOUBLE CRYSTAL
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03312 Å / Relative weight: 1
ReflectionResolution: 1.7→31.3 Å / Num. obs: 11779 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AL4

1al4


Resolution: 1.7→27.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.796 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 604 5.1 %RANDOM
Rwork0.179 ---
obs0.181 11147 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.02 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 105 2 923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9361292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.506586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0162024
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.8251538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1490.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7551.5484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9212736
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6133488
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3774.5554
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 29 -
Rwork0.205 690 -
obs--79.45 %

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