PDB Short entry for 1CCQ HEADER TOXIN 02-MAR-99 1CCQ TITLE NMR STRUCTURE WITH TIGHTLY BOUND WATER MOLECULES OF CYTOTOXIN II TITLE 2 (CARDIOTOXIN) FROM NAJA NAJA OXIANA IN AQUEOUS SOLUTION (MINOR FORM). COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (CYTOTOXIN 2); COMPND 3 CHAIN: A 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 CYTOTOXIN (CARDIOTOXIN), MEMBRANE PERTURBATION, CIS/TRANS KEYWDS 2 ISOMERIZATION, BOUND WATER, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.V.DEMENTIEVA,E.V.BOCHAROV,A.S.ARSENIEV REVDAT 5 27-DEC-23 1CCQ 1 REMARK REVDAT 4 29-NOV-17 1CCQ 1 REMARK HELIX REVDAT 3 24-FEB-09 1CCQ 1 VERSN REVDAT 2 01-APR-03 1CCQ 1 JRNL REVDAT 1 29-JUN-99 1CCQ 0 JRNL AUTH D.V.DEMENTIEVA,E.V.BOCHAROV,A.S.ARSENIEV JRNL TITL TWO FORMS OF CYTOTOXIN II (CARDIOTOXIN) FROM NAJA NAJA JRNL TITL 2 OXIANA IN AQUEOUS SOLUTION: SPATIAL STRUCTURES WITH TIGHTLY JRNL TITL 3 BOUND WATER MOLECULES. JRNL REF EUR.J.BIOCHEM. V. 263 152 1999 JRNL REFN ISSN 0014-2956 JRNL PMID 10429199 JRNL DOI 10.1046/J.1432-1327.1999.00478.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.V.DEMENTIEVA,N.UTKIN YU,A.S.ARSENIEV REMARK 1 TITL SECONDARY STRUCTURE AND CONFORMATIONAL HETEROGENEITY OF REMARK 1 TITL 2 CYTOTOXIN II FROM NAJA NAJA OXIANA REMARK 1 REF RUSS.J.BIOORGANIC CHEM. V. V. 289 1996 REMARK 1 REFN ISSN 1068-1620 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FANTOM 4.0 REMARK 3 AUTHORS : FRACZKIEWICZ, MUMENTHALER, FREYBERG, SCHAUMANN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE RESTRAINED REFINMENT WAS MADE IN REMARK 3 VACUUM AND ONLY FOR PROTEIN SIDE CHAINS. REMARK 4 REMARK 4 1CCQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000574. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY; TOCSY; NOESY; ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY-600 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VARIAN VNMR VNMR, XEASY, DYANA REMARK 210 METHOD USED : SIMULATED ANNEALING BY MOLECULAR REMARK 210 DYNAMICS IN TORSION ANGLE SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 220 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 (TARGET FUNCTION VALUE) REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED BY HOMONUCLEAR NMR REMARK 210 SPECTROSCOPY, USING GRADIENT TECHNIQUE. ROESY EXPERIMENTS WERE REMARK 210 HELD AT 290 AND 318K. 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 VAL A 7 154.91 -42.62 REMARK 500 1 PHE A 10 -146.81 -90.23 REMARK 500 1 VAL A 27 72.58 -66.14 REMARK 500 1 ALA A 28 -42.05 -165.75 REMARK 500 1 ALA A 29 79.81 -119.85 REMARK 500 1 HIS A 31 -49.30 -150.70 REMARK 500 1 LEU A 48 -67.64 -99.87 REMARK 500 1 ASN A 55 50.19 -112.89 REMARK 500 2 LEU A 9 94.85 -60.51 REMARK 500 2 VAL A 27 73.89 -66.43 REMARK 500 2 ALA A 28 -41.77 -168.71 REMARK 500 2 HIS A 31 -47.56 -149.50 REMARK 500 2 VAL A 34 -53.59 -126.49 REMARK 500 2 LEU A 48 -66.81 -96.67 REMARK 500 3 VAL A 7 154.09 -40.50 REMARK 500 3 PHE A 10 -146.25 -89.48 REMARK 500 3 VAL A 27 72.63 -66.39 REMARK 500 3 ALA A 28 -41.98 -166.26 REMARK 500 3 ALA A 29 78.76 -119.97 REMARK 500 3 HIS A 31 -47.81 -152.03 REMARK 500 3 VAL A 34 -61.00 -128.29 REMARK 500 3 LEU A 48 -66.29 -97.38 REMARK 500 3 ASN A 55 53.85 -113.28 REMARK 500 4 LYS A 5 -118.30 -101.77 REMARK 500 4 ASN A 19 14.12 -140.25 REMARK 500 4 VAL A 27 75.03 -67.15 REMARK 500 4 ALA A 28 -41.12 -169.96 REMARK 500 4 HIS A 31 -50.36 -146.81 REMARK 500 4 LEU A 48 -64.26 -90.01 REMARK 500 4 ASN A 55 46.66 -101.59 REMARK 500 5 VAL A 7 156.87 -39.57 REMARK 500 5 LEU A 9 91.91 -173.37 REMARK 500 5 ASN A 19 17.55 -143.88 REMARK 500 5 VAL A 27 74.26 -66.50 REMARK 500 5 ALA A 28 -41.76 -169.91 REMARK 500 5 HIS A 31 -46.27 -148.99 REMARK 500 5 VAL A 34 -52.63 -122.37 REMARK 500 5 LEU A 48 -68.77 -105.60 REMARK 500 5 ASN A 55 49.46 -106.40 REMARK 500 6 VAL A 7 156.39 -47.90 REMARK 500 6 PHE A 10 -147.62 -97.15 REMARK 500 6 ASN A 19 14.20 -140.16 REMARK 500 6 VAL A 27 74.98 -67.95 REMARK 500 6 ALA A 28 -40.67 -171.66 REMARK 500 6 HIS A 31 -47.92 -149.08 REMARK 500 6 VAL A 34 -60.78 -126.61 REMARK 500 6 LEU A 48 -67.47 -91.65 REMARK 500 6 ASN A 55 44.24 -103.89 REMARK 500 6 LYS A 58 48.89 38.27 REMARK 500 7 PHE A 10 -149.63 -89.96 REMARK 500 REMARK 500 THIS ENTRY HAS 158 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1CCQ 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 S1 2 LEU A 1 LEU A 6 0 SHEET 2 S1 2 PHE A 10 CYS A 14 -1 O PHE A 10 N LYS A 5 SHEET 1 S2 3 LYS A 35 ILE A 39 0 SHEET 2 S2 3 LEU A 20 MET A 26 -1 N LEU A 20 O ILE A 39 SHEET 3 S2 3 VAL A 49 ASN A 55 -1 N LYS A 50 O PHE A 25 SSBOND 1 CYS A 3 CYS A 21 1555 1555 1.99 SSBOND 2 CYS A 14 CYS A 38 1555 1555 1.99 SSBOND 3 CYS A 42 CYS A 53 1555 1555 2.05 SSBOND 4 CYS A 54 CYS A 59 1555 1555 2.06 CISPEP 1 VAL A 7 PRO A 8 1 0.03 CISPEP 2 VAL A 7 PRO A 8 2 -0.01 CISPEP 3 VAL A 7 PRO A 8 3 -0.02 CISPEP 4 VAL A 7 PRO A 8 4 0.02 CISPEP 5 VAL A 7 PRO A 8 5 0.01 CISPEP 6 VAL A 7 PRO A 8 6 0.02 CISPEP 7 VAL A 7 PRO A 8 7 0.01 CISPEP 8 VAL A 7 PRO A 8 8 0.02 CISPEP 9 VAL A 7 PRO A 8 9 0.02 CISPEP 10 VAL A 7 PRO A 8 10 0.06 CISPEP 11 VAL A 7 PRO A 8 11 -0.05 CISPEP 12 VAL A 7 PRO A 8 12 -0.04 CISPEP 13 VAL A 7 PRO A 8 13 -0.01 CISPEP 14 VAL A 7 PRO A 8 14 -0.01 CISPEP 15 VAL A 7 PRO A 8 15 -0.03 CISPEP 16 VAL A 7 PRO A 8 16 0.02 CISPEP 17 VAL A 7 PRO A 8 17 -0.01 CISPEP 18 VAL A 7 PRO A 8 18 0.05 CISPEP 19 VAL A 7 PRO A 8 19 -0.06 CISPEP 20 VAL A 7 PRO A 8 20 -0.02 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