PDB Short entry for 1DL0 HEADER TOXIN 08-DEC-99 1DL0 TITLE SOLUTION STRUCTURE OF THE INSECTICIDAL NEUROTOXIN J-ATRACOTOXIN-HV1C COMPND MOL_ID: 1; COMPND 2 MOLECULE: J-ATRACOTOXIN-HV1C; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN THE SPIDER, SOURCE 4 HADRONYCHE VERSUTA. THE PEPTIDE WAS CHEMICALLY SYNTHESIZED FOR NMR SOURCE 5 STUDIES USING STANDARD T-BOC CHEMISTRY AND OXIDIZED/FOLDED IN A SOURCE 6 GLUTATHIONE REDOX BUFFER. KEYWDS NEUROTOXIN, ATRACOTOXIN, INSECTICIDAL, CYSTINE KNOT, VICINAL KEYWDS 2 DISULFIDE, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.H.WANG,G.F.KING REVDAT 4 16-FEB-22 1DL0 1 REMARK REVDAT 3 24-FEB-09 1DL0 1 VERSN REVDAT 2 01-APR-03 1DL0 1 JRNL REVDAT 1 15-SEP-00 1DL0 0 JRNL AUTH X.WANG,M.CONNOR,R.SMITH,M.W.MACIEJEWSKI,M.E.HOWDEN, JRNL AUTH 2 G.M.NICHOLSON,M.J.CHRISTIE,G.F.KING JRNL TITL DISCOVERY AND CHARACTERIZATION OF A FAMILY OF INSECTICIDAL JRNL TITL 2 NEUROTOXINS WITH A RARE VICINAL DISULFIDE BRIDGE. JRNL REF NAT.STRUCT.BIOL. V. 7 505 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10881200 JRNL DOI 10.1038/75921 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.I.FLETCHER,R.SMITH,S.I.O'DONOGHUE,M.NILGES,M.CONNOR, REMARK 1 AUTH 2 M.E.H.HOWDEN,M.J.CHRISTIE,G.F.KING REMARK 1 TITL THE STRUCTURE OF A NOVEL INSECTICIDAL NEUROTOXIN, REMARK 1 TITL 2 OMEGA-ATRACOTOXIN-HV1, FROM THE VENOM OF AN AUSTRALIAN REMARK 1 TITL 3 FUNNEL WEB SPIDER REMARK 1 REF NAT.STRUCT.BIOL. V. 4 559 1997 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.0, X-PLOR 3.8 REMARK 3 AUTHORS : BRUKER ANALYTIK GMBH (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 403 NOE-DERIVED DISTANCE REMARK 3 RESTRAINTS, 41 REMARK 3 DIHEDRAL-ANGLE RESTRAINTS, PLUS 56 RESTRAINTS DEFINING 14 HYDROGEN REMARK 3 BONDS. REMARK 4 REMARK 4 1DL0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010171. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.95 REMARK 210 IONIC STRENGTH : 0.005 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.6 MM J-ATRACOTOXIN-HV1C; 1.6 REMARK 210 MM J-ATRACOTOXIN-HV1C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : H2O 2D NOESY; 2D TOCSY; E-COSY; REMARK 210 D2O 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.0, XEASY 1.3.13, DYANA REMARK 210 1.5, MOLMOL 2.6 REMARK 210 METHOD USED : DYNAMICAL SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR NMR TECHNIQUES. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ARG A 8 H CYS A 32 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 THR A 4 -73.42 -81.27 REMARK 500 1 CYS A 10 170.45 -53.39 REMARK 500 2 THR A 4 -73.70 -79.92 REMARK 500 2 LYS A 34 105.19 -55.22 REMARK 500 2 ASP A 35 -176.98 -60.67 REMARK 500 2 GLU A 36 82.35 -155.13 REMARK 500 3 THR A 4 -72.16 -79.83 REMARK 500 3 ASP A 7 25.48 49.89 REMARK 500 3 CYS A 10 173.21 -56.12 REMARK 500 3 LYS A 34 106.99 -56.39 REMARK 500 4 THR A 4 -71.92 -80.47 REMARK 500 4 CYS A 10 172.86 -53.34 REMARK 500 4 LYS A 34 90.99 -57.31 REMARK 500 5 THR A 4 -72.22 -80.61 REMARK 500 5 ASP A 7 24.97 49.80 REMARK 500 5 CYS A 10 172.26 -53.36 REMARK 500 6 THR A 4 -72.49 -81.04 REMARK 500 6 CYS A 10 173.82 -57.35 REMARK 500 6 GLU A 36 68.41 -155.13 REMARK 500 7 THR A 4 -74.09 -81.46 REMARK 500 7 ASP A 7 25.32 49.15 REMARK 500 7 CYS A 10 173.74 -56.44 REMARK 500 8 CYS A 10 175.35 -56.43 REMARK 500 9 THR A 4 -73.53 -80.56 REMARK 500 10 THR A 4 -71.09 -85.16 REMARK 500 10 ASP A 7 25.07 49.74 REMARK 500 10 CYS A 10 172.11 -55.06 REMARK 500 10 LYS A 34 94.29 -54.84 REMARK 500 11 THR A 4 -76.08 -81.38 REMARK 500 11 ASP A 7 25.62 49.59 REMARK 500 12 THR A 4 -73.10 -80.60 REMARK 500 12 ASP A 7 25.56 48.95 REMARK 500 12 CYS A 10 172.22 -53.94 REMARK 500 12 LYS A 34 94.09 -54.70 REMARK 500 13 THR A 4 -70.71 -79.41 REMARK 500 13 CYS A 10 171.74 -55.11 REMARK 500 14 THR A 4 -73.73 -80.71 REMARK 500 14 CYS A 10 172.18 -55.53 REMARK 500 14 ASP A 35 172.78 -58.27 REMARK 500 15 THR A 4 -71.45 -81.28 REMARK 500 15 CYS A 10 170.68 -54.55 REMARK 500 16 THR A 4 -75.31 -80.35 REMARK 500 16 ASP A 7 25.48 48.98 REMARK 500 16 CYS A 10 170.79 -53.87 REMARK 500 16 LYS A 34 96.87 -54.91 REMARK 500 17 THR A 4 -68.83 -90.36 REMARK 500 17 CYS A 10 171.39 -54.96 REMARK 500 17 GLU A 36 84.31 -154.09 REMARK 500 18 THR A 4 -70.70 -91.52 REMARK 500 18 ASP A 7 24.84 49.85 REMARK 500 REMARK 500 THIS ENTRY HAS 56 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 13 CYS A 14 1 -132.66 REMARK 500 CYS A 13 CYS A 14 2 -135.54 REMARK 500 CYS A 13 CYS A 14 3 -134.72 REMARK 500 CYS A 13 CYS A 14 4 -132.28 REMARK 500 CYS A 13 CYS A 14 5 -134.63 REMARK 500 CYS A 13 CYS A 14 6 -136.47 REMARK 500 CYS A 13 CYS A 14 7 -135.76 REMARK 500 CYS A 13 CYS A 14 8 -136.81 REMARK 500 CYS A 13 CYS A 14 9 -131.26 REMARK 500 CYS A 13 CYS A 14 10 -130.64 REMARK 500 CYS A 13 CYS A 14 11 -134.90 REMARK 500 CYS A 13 CYS A 14 12 -133.64 REMARK 500 CYS A 13 CYS A 14 13 -135.28 REMARK 500 CYS A 13 CYS A 14 14 -134.82 REMARK 500 CYS A 13 CYS A 14 15 -136.20 REMARK 500 CYS A 13 CYS A 14 16 -134.61 REMARK 500 CYS A 13 CYS A 14 17 -137.32 REMARK 500 CYS A 13 CYS A 14 18 -137.35 REMARK 500 CYS A 13 CYS A 14 19 -134.54 REMARK 500 CYS A 13 CYS A 14 20 -134.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 1DL0 A 1 37 UNP P82228 TJT1C_HADVE 1 37 SEQRES 1 A 37 ALA ILE CYS THR GLY ALA ASP ARG PRO CYS ALA ALA CYS SEQRES 2 A 37 CYS PRO CYS CYS PRO GLY THR SER CYS LYS ALA GLU SER SEQRES 3 A 37 ASN GLY VAL SER TYR CYS ARG LYS ASP GLU PRO SHEET 1 A 2 THR A 20 ALA A 24 0 SHEET 2 A 2 SER A 30 LYS A 34 -1 O TYR A 31 N LYS A 23 SSBOND 1 CYS A 3 CYS A 17 1555 1555 2.02 SSBOND 2 CYS A 10 CYS A 22 1555 1555 2.02 SSBOND 3 CYS A 13 CYS A 14 1555 1555 2.02 SSBOND 4 CYS A 16 CYS A 32 1555 1555 2.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000