HEADER ANTIBIOTIC 09-AUG-00 1E68 TITLE SOLUTION STRUCTURE OF BACTERIOCIN AS-48 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AS-48 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BACTERIOCIN AS-48, RESIDUES 36-105; COMPND 5 SYNONYM: BACTERIOCIN AS-4, PEPTIDE ANTIBIOTIC AS-48; COMPND 6 OTHER_DETAILS: PEPTIDE LINK BETWEEN RESIDUES 1 AND 70 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 PLASMID: PMB2 KEYWDS ANTIBIOTIC, BACTERIOCINS, CATIONIC ANTIBACTERIAL PEPTIDES, KEYWDS 2 FIVE-HELIX GLOBULE, CYCLIC POLYPEPTIDE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.GONZALEZ,G.LANGDON,M.BRUIX,A.GALVEZ,E.VALDIVIA,M.MAQUEDA,M.RICO REVDAT 4 03-AUG-11 1E68 1 HEADER COMPND KEYWDS AUTHOR REVDAT 4 2 JRNL REMARK HELIX MASTER REVDAT 4 3 VERSN REVDAT 3 24-FEB-09 1E68 1 VERSN REVDAT 2 26-OCT-00 1E68 1 JRNL REVDAT 1 25-OCT-00 1E68 0 JRNL AUTH C.GONZALEZ,G.LANGDON,M.BRUIX,A.GALVEZ,E.VALDIVIA,M.MAQUEDA, JRNL AUTH 2 M.RICO JRNL TITL BACTERIOCIN AS-48, A MICROBIAL CYCLIC POLYPEPTIDE JRNL TITL 2 STRUCTURALLY AND FUNCTIONALLY RELATED TO MAMMALIAN NK-LYSIN JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 11221 2000 JRNL REFN ISSN 0027-8424 JRNL PMID 11005847 JRNL DOI 10.1073/PNAS.210301097 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.LANGDON,M.BRUIX,A.GALVEZ,E.VALDIVIA,M.MAQUEDA,M.RICO REMARK 1 TITL SEQUENCE-SPECIFIC 1H ASSIGNMENT AND SECONDARY STRUCTURE OF REMARK 1 TITL 2 THE BACTERIOCIN AS-48 CYCLIC PEPTIDE REMARK 1 REF J.BIOMOL.NMR V. 12 173 1998 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 9729795 REMARK 1 DOI 10.1023/A:1008267725043 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA-1.5, GROMOS REMARK 3 AUTHORS : P. GUNTERT ET AL. (DYANA-1.5), VAN GUNSTEREN ET REMARK 3 AL. (GROMOS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE. REMARK 4 REMARK 4 1E68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-00. REMARK 100 THE PDBE ID CODE IS EBI-5241. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, GROMOS REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NONE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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 400 REMARK 400 COMPOUND REMARK 400 PEPTIDE LINK BETWEEN RESIDUES 1 AND 70 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 N MET A 1 C TRP A 70 1.33 REMARK 500 HG11 VAL A 11 HG21 ILE A 31 1.51 REMARK 500 HG12 VAL A 15 HD12 LEU A 55 1.51 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 5 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 VAL A 18 CA - CB - CG1 ANGL. DEV. = 9.1 DEGREES REMARK 500 8 LYS A 61 CB - CG - CD ANGL. DEV. = -17.4 DEGREES REMARK 500 10 ARG A 48 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 12 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 65 N - CA - CB ANGL. DEV. = -12.0 DEGREES REMARK 500 13 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 16 ASN A 17 N - CA - CB ANGL. DEV. = -15.0 DEGREES REMARK 500 16 ASN A 17 OD1 - CG - ND2 ANGL. DEV. = -71.9 DEGREES REMARK 500 16 ASN A 17 CB - CG - ND2 ANGL. DEV. = -37.5 DEGREES REMARK 500 16 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 16 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 19 ARG A 65 N - CA - CB ANGL. DEV. = -14.6 DEGREES REMARK 500 20 ASN A 17 CA - CB - CG ANGL. DEV. = -17.9 DEGREES REMARK 500 20 ASN A 17 OD1 - CG - ND2 ANGL. DEV. = -72.1 DEGREES REMARK 500 20 LYS A 52 CD - CE - NZ ANGL. DEV. = -20.0 DEGREES REMARK 500 20 LYS A 57 CD - CE - NZ ANGL. DEV. = -14.1 DEGREES REMARK 500 20 LYS A 61 CA - CB - CG ANGL. DEV. = -13.4 DEGREES REMARK 500 20 LYS A 61 CD - CE - NZ ANGL. DEV. = -16.4 DEGREES REMARK 500 20 ARG A 65 NE - CZ - NH1 ANGL. DEV. = -3.2 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 ALA A 46 50.16 -144.48 REMARK 500 1 SER A 50 124.95 53.14 REMARK 500 2 TRP A 24 100.60 -57.67 REMARK 500 2 SER A 50 127.49 50.77 REMARK 500 3 SER A 50 125.77 45.86 REMARK 500 3 LYS A 52 -70.05 -55.77 REMARK 500 4 SER A 37 -38.55 76.05 REMARK 500 4 SER A 50 115.14 44.86 REMARK 500 4 ILE A 51 -56.82 -23.88 REMARK 500 5 SER A 50 123.55 49.75 REMARK 500 5 ILE A 51 -49.80 -29.01 REMARK 500 6 SER A 50 120.96 48.33 REMARK 500 7 TRP A 24 99.80 -67.43 REMARK 500 7 SER A 50 116.99 49.37 REMARK 500 8 SER A 37 -37.77 73.39 REMARK 500 8 SER A 50 133.18 50.21 REMARK 500 8 LYS A 52 -71.20 -53.84 REMARK 500 8 LYS A 64 -48.38 -28.48 REMARK 500 9 SER A 50 123.68 50.31 REMARK 500 10 SER A 50 127.09 44.31 REMARK 500 10 LYS A 64 -46.53 -23.41 REMARK 500 11 SER A 37 15.59 -66.58 REMARK 500 11 SER A 50 128.40 43.36 REMARK 500 12 SER A 50 121.45 48.33 REMARK 500 13 SER A 50 121.26 42.15 REMARK 500 13 ILE A 51 -57.75 -27.42 REMARK 500 14 SER A 50 123.62 51.50 REMARK 500 15 SER A 37 -40.38 77.27 REMARK 500 15 SER A 50 118.85 46.63 REMARK 500 16 PRO A 8 38.45 -82.04 REMARK 500 16 ALA A 9 -34.04 53.85 REMARK 500 16 GLU A 49 38.70 -141.15 REMARK 500 16 SER A 50 119.34 53.47 REMARK 500 17 TRP A 24 103.15 -49.60 REMARK 500 17 GLU A 49 37.98 -145.52 REMARK 500 17 SER A 50 133.37 52.96 REMARK 500 18 LYS A 3 -68.54 -91.25 REMARK 500 18 SER A 37 -39.47 70.37 REMARK 500 18 SER A 50 114.32 30.33 REMARK 500 18 ILE A 51 -54.04 -26.99 REMARK 500 19 TRP A 24 98.08 -62.10 REMARK 500 19 SER A 37 5.74 -62.04 REMARK 500 19 SER A 50 126.80 45.85 REMARK 500 19 LYS A 52 -72.05 -57.41 REMARK 500 20 SER A 50 121.69 50.40 REMARK 500 20 LYS A 64 -47.60 -22.42 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 2 ASN A 17 0.07 SIDE CHAIN REMARK 500 5 TYR A 54 0.09 SIDE CHAIN REMARK 500 8 TYR A 54 0.07 SIDE CHAIN REMARK 500 9 TYR A 54 0.09 SIDE CHAIN REMARK 500 11 TYR A 54 0.10 SIDE CHAIN REMARK 500 12 ARG A 48 0.08 SIDE CHAIN REMARK 500 12 TYR A 54 0.07 SIDE CHAIN REMARK 500 13 ARG A 65 0.12 SIDE CHAIN REMARK 500 16 TYR A 54 0.06 SIDE CHAIN REMARK 500 18 TYR A 54 0.08 SIDE CHAIN REMARK 500 20 ASN A 17 0.25 SIDE CHAIN 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 3 ALA A 2 -10.87 REMARK 500 3 GLU A 58 -10.53 REMARK 500 4 ALA A 2 -10.32 REMARK 500 6 GLY A 47 -10.19 REMARK 500 7 GLU A 4 10.11 REMARK 500 7 GLY A 47 -10.02 REMARK 500 9 ALA A 2 -10.09 REMARK 500 10 ALA A 2 -10.75 REMARK 500 12 ALA A 2 -10.39 REMARK 500 12 LYS A 56 -11.52 REMARK 500 13 ALA A 2 -10.27 REMARK 500 14 GLY A 47 -10.18 REMARK 500 14 GLU A 58 -11.57 REMARK 500 16 ALA A 2 -11.22 REMARK 500 16 VAL A 18 -10.10 REMARK 500 17 GLY A 47 -10.10 REMARK 500 17 LYS A 56 -10.17 REMARK 500 18 GLU A 58 -10.03 REMARK 500 20 ALA A 2 -10.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. DBREF 1E68 A 1 70 UNP Q47765 Q47765 36 105 SEQRES 1 A 70 MET ALA LYS GLU PHE GLY ILE PRO ALA ALA VAL ALA GLY SEQRES 2 A 70 THR VAL LEU ASN VAL VAL GLU ALA GLY GLY TRP VAL THR SEQRES 3 A 70 THR ILE VAL SER ILE LEU THR ALA VAL GLY SER GLY GLY SEQRES 4 A 70 LEU SER LEU LEU ALA ALA ALA GLY ARG GLU SER ILE LYS SEQRES 5 A 70 ALA TYR LEU LYS LYS GLU ILE LYS LYS LYS GLY LYS ARG SEQRES 6 A 70 ALA VAL ILE ALA TRP HELIX 1 H1 MET A 1 PHE A 5 1 5 HELIX 2 H2 ALA A 9 ALA A 21 1 13 HELIX 3 H3 VAL A 25 ALA A 34 1 10 HELIX 4 H4 SER A 37 ALA A 45 1 9 HELIX 5 H5 ILE A 51 LYS A 62 1 12 HELIX 6 H6 LYS A 64 TRP A 70 1 7 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