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- PDB-1axh: ATRACOTOXIN-HVI FROM HADRONYCHE VERSUTA (AUSTRALIAN FUNNEL-WEB SP... -

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Basic information

Entry
Database: PDB / ID: 1axh
TitleATRACOTOXIN-HVI FROM HADRONYCHE VERSUTA (AUSTRALIAN FUNNEL-WEB SPIDER, NMR, 20 STRUCTURES
ComponentsATRACOTOXIN-HVI
KeywordsNEUROTOXIN / INSECTICIDAL TOXIN / CYSTINE KNOT / FUNNEL-WEB
Function / homologyOmega-atracotoxin / Omega-atracotoxin, conserved site / Omega-atracotoxin / Omega-atracotoxin (ACTX) type 1 family signature. / calcium channel inhibitor activity / defense response / toxin activity / extracellular region / Omega-hexatoxin-Hv1a
Function and homology information
Biological speciesHadronyche versuta (spider)
MethodSOLUTION NMR / DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING
AuthorsFletcher, J.I. / O'Donoghue, S.I. / Nilges, M. / King, G.F.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: The structure of a novel insecticidal neurotoxin, omega-atracotoxin-HV1, from the venom of an Australian funnel web spider.
Authors: Fletcher, J.I. / Smith, R. / O'Donoghue, S.I. / Nilges, M. / Connor, M. / Howden, M.E. / Christie, M.J. / King, G.F.
#1: Journal: Patent / Year: 1993
Title: Insecticidal Toxins Derived from Funnel Web (Atrax or Hadronyche) Spiders
Authors: Atkinson, R.K. / Tyler, M.I. / Vonarx, E.J. / Howden, M.E.H.
History
DepositionNov 4, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_patent / _citation.title
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATRACOTOXIN-HVI


Theoretical massNumber of molelcules
Total (without water)4,0581
Polymers4,0581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST RESIDUAL RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein/peptide ATRACOTOXIN-HVI / ACTX-HVI


Mass: 4058.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hadronyche versuta (spider) / References: UniProt: P56207
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
141ECOSY

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Sample preparation

Sample conditionspH: 3.6 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
DIANAstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1
Details: INITIAL STRUCTURES (5000) WERE CALCULATED USING THE DISTANCE GEOMETRY PROGRAMME DIANA, USING A SINGLE CYCLE OF REDUNDANT DIHEDRAL ANGLE RESTRAINTS [GUNTERT, P. AND WUTHRICH, K. (1991) J. ...Details: INITIAL STRUCTURES (5000) WERE CALCULATED USING THE DISTANCE GEOMETRY PROGRAMME DIANA, USING A SINGLE CYCLE OF REDUNDANT DIHEDRAL ANGLE RESTRAINTS [GUNTERT, P. AND WUTHRICH, K. (1991) J. BIOMOL. NMR 1, 447-456]. THE 100 STRUCTURES WITH LOWEST RESIDUAL RESTRAINT VIOLATIONS WERE THEN REFINED USING DYNAMICAL SIMULATED ANNEALING [NILGES, M. CLORE, G.M. AND GRONENBORN, A.M. (1988) FEBS LETT. 229, 317-324] IN X-PLOR. STRUCTURES WERE CALCULATED USING 419 NON-REDUNDANT INTERPROTON DISTANCE RESTRAINTS, 43 DIHEDRAL-ANGLE RESTRAINTS (27 PHI, 16 CHI1), AND 28 RESTRAINTS DEFINING 14 HYDROGEN BONDS, GIVING AN AVERAGE OF 13.2 RESTRAINTS/RESIDUE. THE ATOMIC RMS DIFFERENCES FOR RESIDUES 4 - 37 OF THE FINAL FAMILY OF 20 CONFORMERS WITH RESPECT TO THE MEAN COORDINATE POSITIONS ARE 0.22 /- 0.06 AND 0.62 +/- 0.08 ANGSTROMS FOR THE BACKBONE AND HEAVY ATOMS, RESPECTIVELY. THE CORRESPONDING PAIRWISE RMS DIFFERENCES ARE 0.31 +/- 0.07 AND 0.90 +/- 0.12 ANGSTROMS. RESIDUES 1 - 3 ARE DISORDERED. THE DEPOSITED STRUCTURES HAVE BEEN SUPERIMPOSED FOR MINIMUM RMSD OVER THE HEAVY ATOMS OF THE MEAN COORDINATE STRUCTURE. THE FIRST STRUCTURE IS THAT WITH THE LOWEST OVERALL ENERGY IN THE SIMPLIFIED ALL-HYDROGEN CHARMM FORCE FIELD AS IMPLEMENTED IN X-PLOR.
NMR ensembleConformer selection criteria: LOWEST RESIDUAL RESTRAINT VIOLATIONS
Conformers calculated total number: 100 / Conformers submitted total number: 20

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