HEADER TOXIN 27-SEP-04 1WQB TITLE THREE-DIMENSIONAL SOLUTION STRUCUTRE OF APTOTOXIN VII, FROM THE VENOM TITLE 2 OF A TRAP-DOOR SPIDER COMPND MOL_ID: 1; COMPND 2 MOLECULE: APTOTOXIN VII; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PARALYTIC PEPTIDE VII, PP VII; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS CHAMICALLY SYNTHESIZED. THIS SOURCE 4 SEQUENCE OCCURS NATURALLY IN APTOSTICHUS SCHLINGERI. KEYWDS TOXIN, SPIDER'S VENOM, CYSTEIN FRAMEWORK, CYSTINE KNOT MOTIF EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR K.KOBAYASHI,J.-I.KIM,K.SATO,T.KOHNO REVDAT 3 02-MAR-22 1WQB 1 REMARK REVDAT 2 24-FEB-09 1WQB 1 VERSN REVDAT 1 13-DEC-05 1WQB 0 JRNL AUTH K.KOBAYASHI,J.-I.KIM,K.SATO,T.KOHNO JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF APTOTOXIN VII, FROM JRNL TITL 2 THE VENOM OF A TRAP-DOOR SPIDER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 96, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (UXNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 392 RESTRAINTS, 358 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE CONSTRAINTS, 19 DIHEDRAL ANGLE RESTRAINTS, 15 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS AND DISULFIDE BONDS. REMARK 4 REMARK 4 1WQB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000023878. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 3.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM APTOTOXIN; 90% H2O, 10% REMARK 210 D2O; 10MM APTOTOXIN; D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D TOCSY; PE REMARK 210 -COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR 96, X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 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 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: 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 ARG A 6 -164.56 -124.37 REMARK 500 1 LYS A 8 12.67 -145.34 REMARK 500 1 CYS A 11 -168.50 -128.56 REMARK 500 1 CYS A 19 -170.29 -66.56 REMARK 500 1 CYS A 24 101.69 -54.14 REMARK 500 1 SER A 27 -36.59 -159.20 REMARK 500 1 PRO A 31 43.83 -81.52 REMARK 500 2 CYS A 4 -163.19 -161.21 REMARK 500 2 VAL A 7 -70.01 -57.59 REMARK 500 2 LYS A 8 -18.41 -47.40 REMARK 500 2 CYS A 11 -159.32 -116.71 REMARK 500 2 PRO A 17 -166.30 -69.86 REMARK 500 2 CYS A 19 172.67 -48.50 REMARK 500 2 SER A 27 -78.91 -154.05 REMARK 500 3 LEU A 2 -93.05 50.06 REMARK 500 3 ARG A 6 -163.17 -114.40 REMARK 500 3 LYS A 8 32.91 172.20 REMARK 500 3 ALA A 10 104.66 -54.67 REMARK 500 3 CYS A 11 -159.58 -103.18 REMARK 500 3 GLU A 15 -158.27 -108.14 REMARK 500 3 CYS A 19 152.92 -44.47 REMARK 500 3 CYS A 24 90.51 -59.58 REMARK 500 3 SER A 27 -48.25 -160.39 REMARK 500 4 CYS A 4 -152.24 -104.30 REMARK 500 4 VAL A 7 -83.17 -41.86 REMARK 500 4 LYS A 8 -27.52 -36.95 REMARK 500 4 CYS A 11 -162.40 -114.01 REMARK 500 4 PRO A 13 -92.34 -72.16 REMARK 500 4 TRP A 16 95.98 -34.97 REMARK 500 4 PRO A 17 -169.54 -74.61 REMARK 500 4 CYS A 19 155.88 -41.68 REMARK 500 4 CYS A 24 97.37 -57.00 REMARK 500 4 ASP A 25 -96.10 -78.80 REMARK 500 4 SER A 27 -53.75 -160.38 REMARK 500 4 PRO A 31 43.60 -80.66 REMARK 500 5 ALA A 5 -154.19 -101.27 REMARK 500 5 LYS A 8 37.78 -84.90 REMARK 500 5 PRO A 13 -154.14 -69.65 REMARK 500 5 TRP A 14 41.46 -82.22 REMARK 500 5 GLU A 15 -138.51 -91.00 REMARK 500 5 TRP A 16 106.28 -50.05 REMARK 500 5 CYS A 19 169.71 -48.01 REMARK 500 5 CYS A 24 103.56 -57.04 REMARK 500 5 ASP A 25 48.55 -85.33 REMARK 500 5 SER A 27 -58.66 -160.13 REMARK 500 5 PRO A 31 45.01 -81.53 REMARK 500 6 ALA A 5 -158.97 -82.16 REMARK 500 6 ARG A 6 -158.13 -153.20 REMARK 500 6 LYS A 8 -21.33 173.55 REMARK 500 6 GLU A 15 -94.17 -112.33 REMARK 500 REMARK 500 THIS ENTRY HAS 141 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 6 0.22 SIDE CHAIN REMARK 500 2 ARG A 6 0.31 SIDE CHAIN REMARK 500 3 ARG A 6 0.31 SIDE CHAIN REMARK 500 4 ARG A 6 0.31 SIDE CHAIN REMARK 500 6 ARG A 6 0.28 SIDE CHAIN REMARK 500 7 ARG A 6 0.30 SIDE CHAIN REMARK 500 8 ARG A 6 0.19 SIDE CHAIN REMARK 500 9 ARG A 6 0.22 SIDE CHAIN REMARK 500 11 ARG A 6 0.15 SIDE CHAIN REMARK 500 12 ARG A 6 0.32 SIDE CHAIN REMARK 500 13 ARG A 6 0.32 SIDE CHAIN REMARK 500 14 ARG A 6 0.25 SIDE CHAIN REMARK 500 15 ARG A 6 0.16 SIDE CHAIN REMARK 500 16 ARG A 6 0.09 SIDE CHAIN REMARK 500 17 ARG A 6 0.32 SIDE CHAIN REMARK 500 18 ARG A 6 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1WQB A 1 32 UNP P49271 TXP7_APTSC 1 32 SEQRES 1 A 32 TRP LEU GLY CYS ALA ARG VAL LYS GLU ALA CYS GLY PRO SEQRES 2 A 32 TRP GLU TRP PRO CYS CYS SER GLY LEU LYS CYS ASP GLY SEQRES 3 A 32 SER GLU CYS HIS PRO GLN SHEET 1 A 2 LYS A 23 CYS A 24 0 SHEET 2 A 2 CYS A 29 HIS A 30 -1 O HIS A 30 N LYS A 23 SSBOND 1 CYS A 4 CYS A 19 1555 1555 2.02 SSBOND 2 CYS A 11 CYS A 24 1555 1555 2.02 SSBOND 3 CYS A 18 CYS A 29 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 MODEL 1