PDB Short entry for 1FFJ HEADER TOXIN 25-JUL-00 1FFJ TITLE NMR STRUCTURE OF CARDIOTOXIN IN DPC-MICELLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOTOXIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 1; COMPND 5 SYNONYM: CARDIOTOXIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA OXIANA; SOURCE 3 ORGANISM_COMMON: CENTRAL ASIAN COBRA; SOURCE 4 ORGANISM_TAXID: 8657; SOURCE 5 SECRETION: VENOM KEYWDS ALL-BETA SHEET PROTEIN, MEMBRANE PERTURBATION, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.V.DUBOVSKII,D.V.DEMENTIEVA,E.V.BOCHAROV,Y.N.UTKIN,A.S.ARSENIEV REVDAT 4 23-FEB-22 1FFJ 1 REMARK REVDAT 3 24-FEB-09 1FFJ 1 VERSN REVDAT 2 01-APR-03 1FFJ 1 JRNL REVDAT 1 17-JAN-01 1FFJ 0 JRNL AUTH P.V.DUBOVSKII,D.V.DEMENTIEVA,E.V.BOCHAROV,Y.N.UTKIN, JRNL AUTH 2 A.S.ARSENIEV JRNL TITL MEMBRANE BINDING MOTIF OF THE P-TYPE CARDIOTOXIN. JRNL REF J.MOL.BIOL. V. 305 137 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11114253 JRNL DOI 10.1006/JMBI.2000.4283 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.V.DEMENTIEVA,E.V.BOCHAROV,A.S.ARSENIEV REMARK 1 TITL TWO FORMS OF CYTOTOXIN II (CARDIOTOXIN) FROM NAJA NAJA REMARK 1 TITL 2 OXIANA IN AQUEOUS SOLUTION. SPATIAL STRUCTURES WITH TIGHTLY REMARK 1 TITL 3 BOUND WATER MOLECULES REMARK 1 REF EUR.J.BIOCHEM. V. 263 152 1999 REMARK 1 REFN ISSN 0014-2956 REMARK 1 DOI 10.1046/J.1432-1327.1999.00478.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1A, DYANA 1.5 REMARK 3 AUTHORS : VARIAN SOFTWARE (VNMR), GUENTERT, P. & REMARK 3 MUMENTHALER, C. (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF 368 REMARK 3 NOE-DERIVED CONSTRAINTS, 154 DIHEDRAL ANGLE RESTRAINTS, 248 REMARK 3 DISTANCE RESTRAINTS FROM HYDROGEN BONDS AND DISULFIDES REMARK 4 REMARK 4 1FFJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1000011541. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318; 303 REMARK 210 PH : 5.5; 5.5 REMARK 210 IONIC STRENGTH : 0M NACL; 0M NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 3MM CARDIOTOXIN (CYTOTOXIN II); REMARK 210 120 MM PERDEUTERATED REMARK 210 DODECYLPHOSPHOCHOLINE; 3MM REMARK 210 CARDIOTOXIN (CYTOTOXIN II); 120 REMARK 210 MM PERDEUTERATED REMARK 210 DODECYLPHOSPHOCHOLINE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; TOCSY; DQF-COSY; ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.2.11, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 220 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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. SITES OF TIGHTLY BOUND WATER MOLECULES REMARK 210 WERE DETERMINED AS IN DEMENTIEVA ET AL., EUR.J.BIOCHEM.1999,263, REMARK 210 152-162. 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 H MET A 26 O HOH A 61 1.52 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 VAL A 32 87.22 -155.90 REMARK 500 1 ASN A 55 63.75 -105.26 REMARK 500 2 ALA A 28 -38.49 -37.03 REMARK 500 2 VAL A 32 78.58 -157.11 REMARK 500 2 ASN A 55 70.35 -108.13 REMARK 500 3 LEU A 6 -71.70 -40.69 REMARK 500 3 VAL A 32 78.46 -157.41 REMARK 500 3 ASN A 55 63.61 -107.53 REMARK 500 4 VAL A 32 84.04 -153.07 REMARK 500 4 ASN A 55 70.59 -113.87 REMARK 500 5 ALA A 16 155.02 -40.18 REMARK 500 5 ALA A 28 -39.17 -37.14 REMARK 500 5 VAL A 32 84.94 -158.75 REMARK 500 5 ASN A 55 63.38 -118.81 REMARK 500 6 LEU A 6 -70.23 -42.81 REMARK 500 6 ALA A 16 156.07 -48.35 REMARK 500 6 VAL A 32 85.45 -152.21 REMARK 500 7 VAL A 32 74.41 -156.59 REMARK 500 7 ASN A 55 69.03 -103.27 REMARK 500 8 LEU A 6 -73.30 -39.77 REMARK 500 8 ALA A 16 157.77 -42.30 REMARK 500 8 VAL A 32 81.26 -158.35 REMARK 500 9 ALA A 16 157.36 -40.31 REMARK 500 9 HIS A 31 57.54 -142.21 REMARK 500 9 ASN A 55 65.90 -109.77 REMARK 500 10 LEU A 6 -72.13 -40.75 REMARK 500 10 VAL A 32 87.29 -151.68 REMARK 500 10 ASN A 55 66.10 -110.81 REMARK 500 11 ALA A 16 158.74 -44.69 REMARK 500 11 VAL A 32 83.94 -155.12 REMARK 500 12 LYS A 5 -167.04 -75.59 REMARK 500 12 VAL A 32 80.75 -156.59 REMARK 500 12 CYS A 54 143.27 -171.41 REMARK 500 12 ASN A 55 62.12 -103.61 REMARK 500 13 ALA A 16 163.41 -43.49 REMARK 500 13 ASN A 55 66.27 -110.87 REMARK 500 14 VAL A 32 84.02 -157.54 REMARK 500 15 HIS A 31 48.19 -140.28 REMARK 500 15 ASN A 55 66.34 -112.65 REMARK 500 16 ALA A 16 158.07 -40.01 REMARK 500 16 ASN A 55 69.38 -105.70 REMARK 500 17 ALA A 16 151.80 -41.10 REMARK 500 17 ASN A 55 60.88 -108.18 REMARK 500 18 LEU A 6 -73.32 -42.25 REMARK 500 18 ALA A 16 156.09 -43.78 REMARK 500 18 VAL A 32 85.31 -156.95 REMARK 500 18 CYS A 54 139.03 -170.62 REMARK 500 18 ASN A 55 58.01 -101.73 REMARK 500 19 ALA A 16 151.21 -45.88 REMARK 500 19 ALA A 28 -36.95 -36.90 REMARK 500 REMARK 500 THIS ENTRY HAS 57 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CB9 RELATED DB: PDB REMARK 900 1CB9 IS THE SOLUTION STRUCTURE OF CARDIOTOXIN FROM NAJA OXIANA REMARK 900 (MAJOR FORM) DBREF 1FFJ A 1 60 UNP P01441 CX2_NAJOX 1 60 SEQRES 1 A 60 LEU LYS CYS LYS LYS LEU VAL PRO LEU PHE SER LYS THR SEQRES 2 A 60 CYS PRO ALA GLY LYS ASN LEU CYS TYR LYS MET PHE MET SEQRES 3 A 60 VAL ALA ALA PRO HIS VAL PRO VAL LYS ARG GLY CYS ILE SEQRES 4 A 60 ASP VAL CYS PRO LYS SER SER LEU LEU VAL LYS TYR VAL SEQRES 5 A 60 CYS CYS ASN THR ASP LYS CYS ASN FORMUL 2 HOH *2(H2 O) SHEET 1 A 2 LYS A 2 LYS A 4 0 SHEET 2 A 2 SER A 11 THR A 13 -1 N LYS A 12 O CYS A 3 SHEET 1 B 3 PRO A 33 ILE A 39 0 SHEET 2 B 3 LEU A 20 MET A 26 -1 O LEU A 20 N ILE A 39 SHEET 3 B 3 VAL A 49 CYS A 54 -1 N LYS A 50 O PHE A 25 SSBOND 1 CYS A 3 CYS A 21 1555 1555 2.03 SSBOND 2 CYS A 14 CYS A 38 1555 1555 1.98 SSBOND 3 CYS A 42 CYS A 53 1555 1555 2.08 SSBOND 4 CYS A 54 CYS A 59 1555 1555 2.09 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