HEADER TOXIN 14-NOV-97 1AY3 TITLE NODULARIN FROM NODULARIA SPUMIGENA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDIC TOXIN NODULARIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: TOXIN IS CYCLIC PEPTIDE WITH SEQUENCE 2AS-ARG-MFD-GLU- COMPND 5 MDH. ALL PEPTIDIC BONDS ARE NON-STANDARD SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NODULARIA SPUMIGENA; SOURCE 3 ORGANISM_TAXID: 258823; SOURCE 4 STRAIN: BY1 KEYWDS HEPATOTOXIN, INHIBITOR OF SER/THR-SPECIFIC PROTEIN PHOSPHATASES, KEYWDS 2 TOXIN EXPDTA SOLUTION NMR NUMMDL 27 AUTHOR A.J.ANNILA REVDAT 7 15-NOV-23 1AY3 1 SEQADV LINK ATOM REVDAT 6 27-FEB-19 1AY3 1 LINK REVDAT 5 27-JUL-11 1AY3 1 HETNAM HETSYN REMARK REVDAT 4 13-JUL-11 1AY3 1 VERSN REVDAT 3 24-FEB-09 1AY3 1 VERSN REVDAT 2 26-SEP-01 1AY3 3 ATOM REVDAT 1 16-AUG-99 1AY3 0 JRNL AUTH A.ANNILA,J.LEHTIMAKI,K.MATTILA,J.E.ERIKSSON,K.SIVONEN, JRNL AUTH 2 T.T.RANTALA,T.DRAKENBERG JRNL TITL SOLUTION STRUCTURE OF NODULARIN. AN INHIBITOR OF JRNL TITL 2 SERINE/THREONINE-SPECIFIC PROTEIN PHOSPHATASES. JRNL REF J.BIOL.CHEM. V. 271 16695 1996 JRNL REFN ISSN 0021-9258 JRNL PMID 8663277 JRNL DOI 10.1074/JBC.271.28.16695 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : IRMA REMARK 3 AUTHORS : BOELENS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ITERATIVE RELAXATION MATRIX ANALYSIS REMARK 3 T_C = 1.0 NS REMARK 4 REMARK 4 1AY3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000001216. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 274 REMARK 210 PH : 4.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; 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 : FELIXREMARK 210 METHOD METHOD REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 27 REMARK 210 CONFORMERS, SELECTION CRITERIA : RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 22 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TWO-DIMENSIONAL NMR REMARK 210 SPECTROSCOPY ON NON-LABELED NODULARIN 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 400 REMARK 400 COMPOUND REMARK 400 THE SEQUENCE OF NODULARIN MATCHES TO THE SEQUENCE OF NOR00279 IN REMARK 400 NORINE DATABASE, EXCEPT THAT THE STEREO CHEMISTRY OF RESIDUE MFD IS REMARK 400 DIFFERENT FROM THAT OF THE CORRESPONDING RESIDUE 1ZN AS INDICATED REMARK 400 AS ADDA IN NOR00279 SEQUENCE. 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 CG ACB A 1 N ARG A 2 1.38 REMARK 500 N ACB A 1 C MDH A 5 1.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 1 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 2 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 2 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 3 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 3 ARG A 2 CZ ARG A 2 NH2 0.095 REMARK 500 4 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 4 ARG A 2 CZ ARG A 2 NH2 0.096 REMARK 500 5 ARG A 2 CZ ARG A 2 NH1 0.098 REMARK 500 5 ARG A 2 CZ ARG A 2 NH2 0.095 REMARK 500 6 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 6 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 7 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 7 ARG A 2 CZ ARG A 2 NH2 0.095 REMARK 500 8 ARG A 2 CZ ARG A 2 NH1 0.098 REMARK 500 8 ARG A 2 CZ ARG A 2 NH2 0.095 REMARK 500 9 ARG A 2 CZ ARG A 2 NH1 0.098 REMARK 500 9 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 10 ARG A 2 CZ ARG A 2 NH1 0.100 REMARK 500 10 ARG A 2 CZ ARG A 2 NH2 0.095 REMARK 500 11 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 11 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 12 ARG A 2 CZ ARG A 2 NH1 0.098 REMARK 500 12 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 13 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 13 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 14 ARG A 2 CZ ARG A 2 NH1 0.098 REMARK 500 14 ARG A 2 CZ ARG A 2 NH2 0.095 REMARK 500 15 ARG A 2 CZ ARG A 2 NH1 0.098 REMARK 500 15 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 16 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 16 ARG A 2 CZ ARG A 2 NH2 0.095 REMARK 500 17 ARG A 2 CZ ARG A 2 NH1 0.097 REMARK 500 17 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 18 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 18 ARG A 2 CZ ARG A 2 NH2 0.095 REMARK 500 19 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 19 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 20 ARG A 2 CZ ARG A 2 NH1 0.098 REMARK 500 20 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 21 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 21 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 22 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 22 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 23 ARG A 2 CZ ARG A 2 NH1 0.098 REMARK 500 23 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 24 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 24 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 25 ARG A 2 CZ ARG A 2 NH1 0.099 REMARK 500 25 ARG A 2 CZ ARG A 2 NH2 0.094 REMARK 500 REMARK 500 THIS ENTRY HAS 54 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 MFD A 3 CA - C - N ANGL. DEV. = 15.0 DEGREES REMARK 500 3 MFD A 3 CA - C - N ANGL. DEV. = 15.4 DEGREES REMARK 500 4 MFD A 3 CA - C - N ANGL. DEV. = 15.2 DEGREES REMARK 500 5 MFD A 3 CA - C - N ANGL. DEV. = 14.0 DEGREES REMARK 500 6 MFD A 3 CA - C - N ANGL. DEV. = 14.8 DEGREES REMARK 500 7 MFD A 3 CA - C - N ANGL. DEV. = 14.7 DEGREES REMARK 500 8 MFD A 3 CA - C - N ANGL. DEV. = 16.0 DEGREES REMARK 500 9 MFD A 3 CA - C - N ANGL. DEV. = 16.2 DEGREES REMARK 500 10 MFD A 3 CA - C - N ANGL. DEV. = 14.9 DEGREES REMARK 500 11 MFD A 3 CA - C - N ANGL. DEV. = 15.0 DEGREES REMARK 500 12 MFD A 3 CA - C - N ANGL. DEV. = 15.1 DEGREES REMARK 500 13 MFD A 3 CA - C - N ANGL. DEV. = 15.1 DEGREES REMARK 500 14 MFD A 3 CA - C - N ANGL. DEV. = 14.6 DEGREES REMARK 500 15 MFD A 3 CA - C - N ANGL. DEV. = 15.1 DEGREES REMARK 500 16 MFD A 3 CA - C - N ANGL. DEV. = 15.6 DEGREES REMARK 500 17 MFD A 3 CA - C - N ANGL. DEV. = 17.4 DEGREES REMARK 500 18 MFD A 3 CA - C - N ANGL. DEV. = 16.9 DEGREES REMARK 500 19 MFD A 3 CA - C - N ANGL. DEV. = 18.0 DEGREES REMARK 500 20 MFD A 3 CA - C - N ANGL. DEV. = 14.5 DEGREES REMARK 500 21 MFD A 3 CA - C - N ANGL. DEV. = 15.4 DEGREES REMARK 500 22 MFD A 3 CA - C - N ANGL. DEV. = 15.4 DEGREES REMARK 500 23 MFD A 3 CA - C - N ANGL. DEV. = 15.1 DEGREES REMARK 500 24 MFD A 3 CA - C - N ANGL. DEV. = 13.5 DEGREES REMARK 500 25 MFD A 3 CA - C - N ANGL. DEV. = 15.3 DEGREES REMARK 500 26 MFD A 3 CA - C - N ANGL. DEV. = 15.3 DEGREES REMARK 500 27 MFD A 3 CA - C - N ANGL. DEV. = 16.2 DEGREES 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 MFD A 3 FGA A 4 1 128.06 REMARK 500 MFD A 3 FGA A 4 2 136.68 REMARK 500 MFD A 3 FGA A 4 3 135.29 REMARK 500 MFD A 3 FGA A 4 4 134.63 REMARK 500 MFD A 3 FGA A 4 5 130.32 REMARK 500 MFD A 3 FGA A 4 6 133.76 REMARK 500 MFD A 3 FGA A 4 7 135.15 REMARK 500 MFD A 3 FGA A 4 8 136.65 REMARK 500 MFD A 3 FGA A 4 9 134.31 REMARK 500 MFD A 3 FGA A 4 10 134.45 REMARK 500 MFD A 3 FGA A 4 11 135.08 REMARK 500 MFD A 3 FGA A 4 12 131.68 REMARK 500 MFD A 3 FGA A 4 13 131.82 REMARK 500 MFD A 3 FGA A 4 14 131.87 REMARK 500 MFD A 3 FGA A 4 15 131.17 REMARK 500 MFD A 3 FGA A 4 16 135.66 REMARK 500 MFD A 3 FGA A 4 17 137.59 REMARK 500 MFD A 3 FGA A 4 18 133.57 REMARK 500 MFD A 3 FGA A 4 19 136.98 REMARK 500 MFD A 3 FGA A 4 20 130.69 REMARK 500 MFD A 3 FGA A 4 21 135.70 REMARK 500 MFD A 3 FGA A 4 22 134.63 REMARK 500 MFD A 3 FGA A 4 23 130.61 REMARK 500 MFD A 3 FGA A 4 24 128.92 REMARK 500 MFD A 3 FGA A 4 25 135.44 REMARK 500 MFD A 3 FGA A 4 26 135.52 REMARK 500 MFD A 3 FGA A 4 27 134.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 MFD A 3 -20.73 REMARK 500 2 MFD A 3 -20.01 REMARK 500 3 MFD A 3 -20.03 REMARK 500 4 MFD A 3 -20.23 REMARK 500 5 MFD A 3 -20.88 REMARK 500 6 MFD A 3 -20.37 REMARK 500 7 MFD A 3 -20.15 REMARK 500 8 MFD A 3 -19.93 REMARK 500 9 MFD A 3 -20.00 REMARK 500 10 MFD A 3 -20.18 REMARK 500 11 MFD A 3 -20.15 REMARK 500 12 MFD A 3 -20.75 REMARK 500 13 MFD A 3 -20.64 REMARK 500 14 MFD A 3 -20.65 REMARK 500 15 MFD A 3 -20.58 REMARK 500 16 MFD A 3 -20.06 REMARK 500 17 MFD A 3 -19.50 REMARK 500 18 MFD A 3 -20.25 REMARK 500 19 MFD A 3 -19.44 REMARK 500 20 MFD A 3 -20.59 REMARK 500 21 MFD A 3 -20.00 REMARK 500 22 MFD A 3 -20.20 REMARK 500 23 MFD A 3 -20.76 REMARK 500 24 MFD A 3 -20.74 REMARK 500 25 MFD A 3 -20.04 REMARK 500 26 MFD A 3 -20.08 REMARK 500 27 MFD A 3 -19.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AY3 A 1 5 NOR NOR00279 NOR00279 1 5 SEQADV 1AY3 MFD A 3 NOR NOR00279 1ZN 3 CONFLICT SEQRES 1 A 5 ACB ARG MFD FGA MDH HET ACB A 1 15 HET MFD A 3 50 HET FGA A 4 14 HET MDH A 5 14 HETNAM ACB 3-METHYL-BETA-D-ASPARTIC ACID HETNAM MFD (2S,3S,8S,9S)-3-AMINO-9-METHOXY-2,6,8-TRIMETHYL-10- HETNAM 2 MFD PHENYLDECA-4,6-DIENOIC ACID HETNAM FGA GAMMA-D-GLUTAMIC ACID HETNAM MDH N-METHYLDEHYDROBUTYRINE HETSYN ACB (3S)-3-METHYL-D-ASPARTIC ACID; D-METHYL ASPARTIC ACID HETSYN FGA D-GLUTAMIC ACID FORMUL 1 ACB C5 H9 N O4 FORMUL 1 MFD C20 H29 N O3 FORMUL 1 FGA C5 H9 N O4 FORMUL 1 MDH C5 H9 N O2 LINK C ACB A 1 N ARG A 2 1555 1555 3.86 LINK C ARG A 2 N MFD A 3 1555 1555 1.39 LINK C MFD A 3 N FGA A 4 1555 1555 1.39 LINK CD FGA A 4 N MDH A 5 1555 1555 1.42 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 HETATM 1 C ACB A 1 -0.610 0.037 3.178 1.00 0.00 C HETATM 2 O ACB A 1 -1.135 0.763 4.029 1.00 0.00 O HETATM 3 OXT ACB A 1 -0.953 -0.151 2.007 1.00 0.00 O HETATM 4 CA ACB A 1 0.683 -0.729 3.640 1.00 0.00 C HETATM 5 N ACB A 1 1.767 0.230 3.352 1.00 0.00 N HETATM 6 CB ACB A 1 0.822 -2.144 2.944 1.00 0.00 C HETATM 7 CG ACB A 1 1.586 -2.082 1.612 1.00 0.00 C HETATM 8 C4 ACB A 1 1.478 -3.237 3.808 1.00 0.00 C HETATM 9 OD2 ACB A 1 2.800 -1.870 1.593 1.00 0.00 O HETATM 10 HA ACB A 1 0.651 -0.865 4.732 1.00 0.00 H HETATM 11 H ACB A 1 2.293 0.070 2.504 1.00 0.00 H HETATM 12 HB3 ACB A 1 -0.211 -2.502 2.762 1.00 0.00 H HETATM 13 H41 ACB A 1 0.893 -3.388 4.729 1.00 0.00 H HETATM 14 H42 ACB A 1 2.505 -2.967 4.097 1.00 0.00 H HETATM 15 H43 ACB A 1 1.509 -4.192 3.260 1.00 0.00 H