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- PDB-1m24: Trichotoxin_A50E, An Ion Channel-Forming Polypeptide -

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Basic information

Entry
Database: PDB / ID: 1m24
TitleTrichotoxin_A50E, An Ion Channel-Forming Polypeptide
ComponentsTRICHOTOXIN_A50E
KeywordsANTIBIOTIC / TRICHOTOXIN / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL
Function / homologyTRICHOTOXIN A50E / ACETONITRILE / :
Function and homology information
Biological speciesTRICHODERMA VIRIDE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsChugh, J.K. / Brueckner, H. / Wallace, B.A.
CitationJournal: Biochemistry / Year: 2002
Title: Model for a Helical Bundle Channel Based on the High-Resolution Crystal Structure of Trichotoxin_A50E
Authors: Chugh, J.K. / Brueckner, H. / Wallace, B.A.
History
DepositionJun 21, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: 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 1.4Sep 5, 2012Group: Derived calculations
Revision 1.5Dec 12, 2012Group: Other
Revision 1.6Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 2.1Apr 3, 2024Group: 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: TRICHOTOXIN_A50E
B: TRICHOTOXIN_A50E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4304
Polymers3,3482
Non-polymers822
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRICHOTOXIN_A50E
hetero molecules

B: TRICHOTOXIN_A50E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4304
Polymers3,3482
Non-polymers822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area820 Å2
ΔGint-7 kcal/mol
Surface area3660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)9.490, 16.850, 31.680
Angle α, β, γ (deg.)95.77, 98.07, 99.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide TRICHOTOXIN_A50E


Type: Peptaibol / Class: Antibiotic / Mass: 1674.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: TRICHOTOXIN_A50E IS AN OCTADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Source: (natural) TRICHODERMA VIRIDE (fungus) / Strain: NRRL 5242 / References: NOR: NOR01101, TRICHOTOXIN A50E
#2: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRICHOTOXIN_A50E IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...TRICHOTOXIN_A50E IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, TRICHOTOXIN_A50E 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: 1.3 Å3/Da / Density % sol: 8.28 %
Crystal growDetails: METHANOL:ACETONITRILE 1:10, EVAPORATION, RECRYSTALLIZATION, TEMPERATURE 268K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
Conc.: 29.6 mg/ml / Common name: peptide

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 0.6883
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 2001
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6883 Å / Relative weight: 1
ReflectionResolution: 0.9→10 Å / Num. obs: 13427 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 2.79 % / Rmerge(I) obs: 0.0514 / Net I/σ(I): 15.03
Reflection shellResolution: 0.9→0.95 Å / Redundancy: 2.18 % / Rmerge(I) obs: 0.2614 / Mean I/σ(I) obs: 2.36 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 10 Å / Rmerge(I) obs: 0.0514
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.261

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Processing

Software
NameVersionClassification
MOLREPphasing
ARP/wARPmodel building
SHELXL-97refinement
SMARTV. 5.054 (BRUKER)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL OF HELICAL PEPTIDE, RESIDUES 1-13.

Resolution: 0.9→10 Å / Num. parameters: 2244 / Num. restraintsaints: 2814 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE, NO RESTRAINTS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.092 688 5.1 %RANDOM
all0.076 13427 --
obs0.075 -99.7 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 278 / Occupancy sum non hydrogen: 249
Refinement stepCycle: LAST / Resolution: 0.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms238 0 6 5 249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_non_zero_chiral_vol1.186
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.091
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.9 Å / Rfactor all: 0.0762 / Rfactor obs: 0.0762 / Rfactor Rfree: 0.092 / Rfactor Rwork: 0.075
Solvent computation
*PLUS
Displacement parameters
*PLUS

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