HEADER TOXIN 11-JUN-98 1BH1 TITLE STRUCTURAL STUDIES OF D-PRO MELITTIN, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: MELITTIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: APIS MELLIFERA; SOURCE 3 ORGANISM_COMMON: HONEY BEE; SOURCE 4 ORGANISM_TAXID: 7460 KEYWDS TOXIN, HEMOLYTIC POLYPEPTIDE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.J.BARNHAM,D.HEWISH,J.WERKMEISTER,C.CURTAIN,A.KIRKPATRICK, AUTHOR 2 N.BARTONE,S.T.LIU,R.NORTON,D.RIVETT REVDAT 3 24-FEB-09 1BH1 1 VERSN REVDAT 2 16-FEB-99 1BH1 1 SOURCE COMPND REMARK TITLE REVDAT 2 2 1 SEQRES AUTHOR REVDAT 1 06-JAN-99 1BH1 0 JRNL AUTH D.R.HEWISH,K.J.BARNHAM,J.A.WERKMEISTER, JRNL AUTH 2 A.KIRKPATRICK,N.BARTONE,S.T.LIU,R.S.NORTON, JRNL AUTH 3 C.CURTAIN,D.E.RIVETTA JRNL TITL STRUCTURE AND ACTIVITY OF D-PRO14 MELITTIN. JRNL REF J.PROTEIN CHEM. V. 21 243 2002 JRNL REFN ISSN 0277-8033 JRNL PMID 12168695 JRNL DOI 10.1023/A:1019741202601 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1000 STRUCTURES WERE INITIALLY REMARK 3 GENERATED USING THE DISTANCE GEOMETRY PROGRAM DYANA 1.4. THESE REMARK 3 STRUCTURES WERE REFINED USING SIMULATED ANNEALING IN X-PLOR3.8 REMARK 3 WITH THE DISTANCE GEOMETRY FORCE FIELD, THEN ENERGY MINIMIZED REMARK 3 USING THE CHARMM FORCE FIELD WITH A DISTANCE-DEPENDENT REMARK 3 DILECTRIC. THE 20 BEST STRUCTURES BASED ON THEIR REMARK 3 STEREOCHEMICAL AND NOE ENERGIES WERE CHOSEN FOR ANALYSIS. REMARK 4 REMARK 4 1BH1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277 REMARK 210 PH : 5.2 REMARK 210 IONIC STRENGTH : 2MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : METHANOL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, COSY, E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 1.4, X-PLOR 3.8 REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST STEREOCHEMICAL AND NOE REMARK 210 ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D NMR SPECTROSCOPY 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 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 1 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 3 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 5 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 5 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 7 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 7 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 8 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 8 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 9 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 9 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 10 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 12 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 12 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 13 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 14 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 15 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 17 ARG A 22 NH1 - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 17 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 18 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 19 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 20 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 20 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES 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 11 -76.65 -121.24 REMARK 500 1 LEU A 13 70.95 179.41 REMARK 500 1 PRO A 14 -86.64 59.31 REMARK 500 1 LEU A 16 -39.68 -38.52 REMARK 500 1 TRP A 19 -63.11 -102.25 REMARK 500 1 GLN A 25 66.70 -100.18 REMARK 500 2 ILE A 2 -119.03 -120.38 REMARK 500 2 LEU A 13 63.40 -156.26 REMARK 500 2 PRO A 14 -100.85 61.26 REMARK 500 2 TRP A 19 -61.44 -101.59 REMARK 500 3 ILE A 2 -154.36 -116.54 REMARK 500 3 VAL A 5 -33.74 -29.86 REMARK 500 3 THR A 11 -61.49 -120.08 REMARK 500 3 LEU A 13 32.88 -150.32 REMARK 500 3 PRO A 14 175.54 94.77 REMARK 500 3 ALA A 15 -25.30 -26.74 REMARK 500 3 TRP A 19 -78.40 -101.36 REMARK 500 4 THR A 11 -61.88 -122.95 REMARK 500 4 LEU A 13 61.01 -150.55 REMARK 500 4 PRO A 14 -99.04 62.88 REMARK 500 4 TRP A 19 -61.10 -101.53 REMARK 500 4 ARG A 24 1.60 -52.97 REMARK 500 5 LEU A 13 66.23 -163.15 REMARK 500 5 PRO A 14 -85.75 58.16 REMARK 500 5 TRP A 19 -70.98 -102.05 REMARK 500 6 THR A 11 -63.09 -121.65 REMARK 500 6 LEU A 13 65.33 179.52 REMARK 500 6 PRO A 14 -93.04 60.19 REMARK 500 6 TRP A 19 -67.28 -102.30 REMARK 500 6 ARG A 24 -9.94 -47.88 REMARK 500 7 THR A 11 -78.97 -120.84 REMARK 500 7 LEU A 13 79.86 179.15 REMARK 500 7 PRO A 14 -99.66 64.07 REMARK 500 7 TRP A 19 -69.62 -101.37 REMARK 500 7 ARG A 22 -60.38 -90.02 REMARK 500 8 THR A 11 -64.64 -106.84 REMARK 500 8 LEU A 13 67.27 -152.64 REMARK 500 8 PRO A 14 -81.31 56.84 REMARK 500 8 TRP A 19 -69.88 -101.89 REMARK 500 9 PRO A 14 -83.65 61.56 REMARK 500 9 TRP A 19 -64.30 -102.77 REMARK 500 10 VAL A 5 -30.80 -28.28 REMARK 500 10 LEU A 13 57.78 -169.72 REMARK 500 10 PRO A 14 -102.90 59.08 REMARK 500 10 TRP A 19 -74.82 -100.75 REMARK 500 10 ARG A 22 -62.23 -90.67 REMARK 500 10 ARG A 24 -18.82 -47.17 REMARK 500 11 LEU A 13 68.19 -152.13 REMARK 500 11 PRO A 14 -83.19 54.15 REMARK 500 11 TRP A 19 -67.57 -101.58 REMARK 500 11 ARG A 22 -68.71 -91.54 REMARK 500 12 THR A 11 -61.92 -107.08 REMARK 500 12 LEU A 13 58.89 -159.45 REMARK 500 12 PRO A 14 -92.89 55.94 REMARK 500 12 TRP A 19 -70.67 -100.93 REMARK 500 13 ILE A 2 52.77 -112.95 REMARK 500 13 LEU A 13 100.86 -58.51 REMARK 500 13 PRO A 14 -84.82 31.89 REMARK 500 13 TRP A 19 -64.09 -100.75 REMARK 500 14 LEU A 13 61.25 179.44 REMARK 500 14 PRO A 14 -73.46 50.92 REMARK 500 14 TRP A 19 -71.33 -101.22 REMARK 500 15 LEU A 13 60.71 -160.74 REMARK 500 15 PRO A 14 -80.10 52.95 REMARK 500 15 TRP A 19 -63.21 -102.15 REMARK 500 16 ILE A 2 75.64 -110.86 REMARK 500 16 LEU A 13 65.13 -179.49 REMARK 500 16 PRO A 14 -78.61 51.33 REMARK 500 16 TRP A 19 -69.08 -101.08 REMARK 500 17 ILE A 2 -125.37 -126.02 REMARK 500 17 VAL A 5 -34.98 -35.53 REMARK 500 17 LEU A 13 69.43 179.05 REMARK 500 17 PRO A 14 -76.91 42.09 REMARK 500 17 TRP A 19 -64.21 -100.98 REMARK 500 18 THR A 11 -63.10 -122.18 REMARK 500 18 LEU A 13 55.88 -158.88 REMARK 500 18 PRO A 14 -86.03 52.11 REMARK 500 18 TRP A 19 -70.81 -101.13 REMARK 500 19 THR A 11 -64.37 -121.83 REMARK 500 19 LEU A 13 60.53 -171.09 REMARK 500 19 PRO A 14 -82.77 41.78 REMARK 500 19 TRP A 19 -64.72 -101.22 REMARK 500 20 LEU A 9 6.16 -64.50 REMARK 500 20 LEU A 13 60.91 -178.42 REMARK 500 20 PRO A 14 -75.31 53.87 REMARK 500 20 TRP A 19 -66.73 -100.96 REMARK 500 20 ARG A 22 -76.59 -90.40 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 22 0.30 SIDE_CHAIN REMARK 500 1 ARG A 24 0.30 SIDE_CHAIN REMARK 500 2 ARG A 22 0.31 SIDE_CHAIN REMARK 500 2 ARG A 24 0.27 SIDE_CHAIN REMARK 500 3 ARG A 22 0.20 SIDE_CHAIN REMARK 500 3 ARG A 24 0.28 SIDE_CHAIN REMARK 500 4 ARG A 22 0.31 SIDE_CHAIN REMARK 500 4 ARG A 24 0.32 SIDE_CHAIN REMARK 500 5 ARG A 22 0.30 SIDE_CHAIN REMARK 500 5 ARG A 24 0.31 SIDE_CHAIN REMARK 500 6 ARG A 22 0.30 SIDE_CHAIN REMARK 500 6 ARG A 24 0.31 SIDE_CHAIN REMARK 500 7 ARG A 22 0.30 SIDE_CHAIN REMARK 500 7 ARG A 24 0.32 SIDE_CHAIN REMARK 500 8 ARG A 22 0.27 SIDE_CHAIN REMARK 500 8 ARG A 24 0.30 SIDE_CHAIN REMARK 500 9 ARG A 22 0.30 SIDE_CHAIN REMARK 500 9 ARG A 24 0.32 SIDE_CHAIN REMARK 500 10 ARG A 22 0.29 SIDE_CHAIN REMARK 500 10 ARG A 24 0.30 SIDE_CHAIN REMARK 500 11 ARG A 22 0.32 SIDE_CHAIN REMARK 500 11 ARG A 24 0.28 SIDE_CHAIN REMARK 500 12 ARG A 22 0.30 SIDE_CHAIN REMARK 500 12 ARG A 24 0.31 SIDE_CHAIN REMARK 500 13 ARG A 22 0.27 SIDE_CHAIN REMARK 500 13 ARG A 24 0.31 SIDE_CHAIN REMARK 500 14 ARG A 22 0.32 SIDE_CHAIN REMARK 500 14 ARG A 24 0.30 SIDE_CHAIN REMARK 500 15 ARG A 22 0.09 SIDE_CHAIN REMARK 500 15 ARG A 24 0.32 SIDE_CHAIN REMARK 500 16 ARG A 22 0.28 SIDE_CHAIN REMARK 500 16 ARG A 24 0.28 SIDE_CHAIN REMARK 500 17 ARG A 22 0.32 SIDE_CHAIN REMARK 500 17 ARG A 24 0.31 SIDE_CHAIN REMARK 500 18 ARG A 22 0.31 SIDE_CHAIN REMARK 500 18 ARG A 24 0.30 SIDE_CHAIN REMARK 500 19 ARG A 22 0.32 SIDE_CHAIN REMARK 500 19 ARG A 24 0.31 SIDE_CHAIN REMARK 500 20 ARG A 22 0.13 SIDE_CHAIN REMARK 500 20 ARG A 24 0.31 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 1 PRO A 14 121.7 ALPHA-CARBON REMARK 500 2 PRO A 14 120.6 ALPHA-CARBON REMARK 500 3 PRO A 14 121.9 ALPHA-CARBON REMARK 500 4 PRO A 14 120.5 ALPHA-CARBON REMARK 500 5 PRO A 14 121.8 ALPHA-CARBON REMARK 500 6 PRO A 14 121.2 ALPHA-CARBON REMARK 500 7 PRO A 14 121.7 ALPHA-CARBON REMARK 500 8 PRO A 14 122.1 ALPHA-CARBON REMARK 500 9 PRO A 14 121.9 ALPHA-CARBON REMARK 500 10 PRO A 14 120.6 ALPHA-CARBON REMARK 500 11 PRO A 14 122.3 ALPHA-CARBON REMARK 500 12 PRO A 14 121.1 ALPHA-CARBON REMARK 500 13 PRO A 14 123.7 ALPHA-CARBON REMARK 500 14 PRO A 14 121.7 ALPHA-CARBON REMARK 500 15 PRO A 14 121.7 ALPHA-CARBON REMARK 500 16 PRO A 14 122.1 ALPHA-CARBON REMARK 500 17 PRO A 14 122.7 ALPHA-CARBON REMARK 500 18 PRO A 14 122.2 ALPHA-CARBON REMARK 500 19 PRO A 14 122.7 ALPHA-CARBON REMARK 500 20 PRO A 14 122.5 ALPHA-CARBON REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 27 DBREF 1BH1 A 1 26 UNP P01501 MEL_APIME 44 69 SEQRES 1 A 27 GLY ILE GLY ALA VAL LEU LYS VAL LEU THR THR GLY LEU SEQRES 2 A 27 PRO ALA LEU ILE SER TRP ILE LYS ARG LYS ARG GLN GLN SEQRES 3 A 27 NH2 HET NH2 A 27 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 1 VAL A 5 VAL A 8 1 4 HELIX 2 2 LEU A 16 TRP A 19 1 4 HELIX 3 3 LYS A 21 ARG A 24 1 4 LINK N NH2 A 27 C GLN A 26 1555 1555 1.30 SITE 1 AC1 1 GLN A 26 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 292 0 1 3 0 0 1 6 0 0 0 3 END