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Yorodumi- PDB-1axh: ATRACOTOXIN-HVI FROM HADRONYCHE VERSUTA (AUSTRALIAN FUNNEL-WEB SP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1axh | ||||||
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Title | ATRACOTOXIN-HVI FROM HADRONYCHE VERSUTA (AUSTRALIAN FUNNEL-WEB SPIDER, NMR, 20 STRUCTURES | ||||||
Components | ATRACOTOXIN-HVI | ||||||
Keywords | NEUROTOXIN / INSECTICIDAL TOXIN / CYSTINE KNOT / FUNNEL-WEB | ||||||
Function / homology | Omega-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 species | Hadronyche versuta (spider) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING | ||||||
Authors | Fletcher, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1axh.cif.gz | 204.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1axh.ent.gz | 178.5 KB | Display | PDB format |
PDBx/mmJSON format | 1axh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1axh_validation.pdf.gz | 348.9 KB | Display | wwPDB validaton report |
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Full document | 1axh_full_validation.pdf.gz | 477.7 KB | Display | |
Data in XML | 1axh_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1axh_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1axh ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1axh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 3.6 / Temperature: 298 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: 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 ensemble | Conformer selection criteria: LOWEST RESIDUAL RESTRAINT VIOLATIONS Conformers calculated total number: 100 / Conformers submitted total number: 20 |