PDB Short entry for 1T5N HEADER ANTIBIOTIC 04-MAY-04 1T5N TITLE STRUCTURAL TRANSITIONS AS DETERMINANTS OF CALCIUM-DEPENDENT ANTIBIOTIC TITLE 2 DAPTOMYCIN CAVEAT 1T5N THR A 5 C-BETA WRONG HAND IN ALL MODELS, THR A 5 C-ALPHA CAVEAT 2 1T5N WRONG HAND IN ALL MODELS, LME A 13 C-BETA WRONG HAND IN ALL CAVEAT 3 1T5N MODELS, KYN A 14 C-ALPHA WRONG HAND IN ALL MODELS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DAPTOMYCIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: A21978C, CUBICIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOMYCES ROSEOSPORUS; SOURCE 4 ORGANISM_TAXID: 67294 KEYWDS DAPTOMYCIN, CUBICIN, ANTIBIOTIC, LIPOPEPTIDE, CALCIUM-DEPENDENT EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR D.JUNG,A.ROZEK,M.OKON,R.E.HANCOCK REVDAT 5 06-NOV-19 1T5N 1 REMARK LINK REVDAT 4 27-JUL-11 1T5N 1 ATOM CAVEAT REMARK REVDAT 3 13-JUL-11 1T5N 1 VERSN REVDAT 2 24-FEB-09 1T5N 1 VERSN REVDAT 1 31-AUG-04 1T5N 0 JRNL AUTH D.JUNG,A.ROZEK,M.OKON,R.E.HANCOCK JRNL TITL STRUCTURAL TRANSITIONS AS DETERMINANTS OF THE ACTION OF THE JRNL TITL 2 CALCIUM-DEPENDENT ANTIBIOTIC DAPTOMYCIN. JRNL REF CHEM.BIOL. V. 11 949 2004 JRNL REFN ISSN 1074-5521 JRNL PMID 15271353 JRNL DOI 10.1016/J.CHEMBIOL.2004.04.020 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DGII MODULE OF INSIGHT II VER. 97.2 REMARK 3 AUTHORS : ACCYLRYS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T5N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022342. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308.15 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 100MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM DAPTOMYCIN, 100MM KCL, 5MM REMARK 210 CACL2, 0.2MM EDTA, 93% H2O, 7% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DGII MODULE OF INSIGHT II VER. REMARK 210 97.2, NMRPIPE 1, NMRDRAW 5.0.4 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 DAPTOMYCIN IS A CYCLIC TRIDECAMER LIPOPETIDE. REMARK 400 HERE, DAPTOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE REMARK 400 SEQUENCE (SEQRES) AND ONE LIGAND (HET) DKA. REMARK 400 REMARK 400 THE DAPTOMYCIN IS CYCLIC LIPOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: DAPTOMYCIN REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE DKA REMARK 400 DESCRIPTION: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE REMARK 400 SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N- REMARK 400 TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING REMARK 400 DERIVED FROM CYCLISATION OF THR3 SIDE CHAIN ONTO THE REMARK 400 C-TER CARBOXYL GROUP THE N-DECANOYL FATTY ACID IS REMARK 400 LINKED TO THE MAIN BODY OF THE MOLECULE VIA N-TERM REMARK 400 ACYLATION. 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 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 1 DSN A 12 CB - CA - C ANGL. DEV. = 16.8 DEGREES REMARK 500 2 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 2 DSN A 12 CB - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 3 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 3 DSN A 12 CB - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 4 TRP A 2 CB - CA - C ANGL. DEV. = 12.5 DEGREES REMARK 500 4 DAL A 9 N - CA - CB ANGL. DEV. = 9.5 DEGREES REMARK 500 4 DSN A 12 CB - CA - C ANGL. DEV. = 15.5 DEGREES REMARK 500 5 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES REMARK 500 5 DSN A 12 CB - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 6 DAL A 9 N - CA - CB ANGL. DEV. = 9.8 DEGREES REMARK 500 6 DSN A 12 CB - CA - C ANGL. DEV. = 16.0 DEGREES REMARK 500 7 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES REMARK 500 7 DSN A 12 CB - CA - C ANGL. DEV. = 17.7 DEGREES REMARK 500 8 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 8 DSN A 12 CB - CA - C ANGL. DEV. = 17.3 DEGREES REMARK 500 9 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 9 DSN A 12 CB - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 10 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 10 DSN A 12 CB - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 11 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 11 DSN A 12 CB - CA - C ANGL. DEV. = 15.8 DEGREES REMARK 500 12 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES REMARK 500 12 DSN A 12 CB - CA - C ANGL. DEV. = 15.5 DEGREES REMARK 500 13 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES REMARK 500 13 DSN A 12 CB - CA - C ANGL. DEV. = 17.0 DEGREES REMARK 500 14 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 14 DSN A 12 CB - CA - C ANGL. DEV. = 17.7 DEGREES REMARK 500 15 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES REMARK 500 15 DSN A 12 CB - CA - C ANGL. DEV. = 15.8 DEGREES REMARK 500 16 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 16 DSN A 12 CB - CA - C ANGL. DEV. = 16.6 DEGREES REMARK 500 17 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES REMARK 500 17 DSN A 12 CB - CA - C ANGL. DEV. = 16.5 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 DSG A 3 -34.83 148.43 REMARK 500 1 ASP A 4 -112.55 -77.94 REMARK 500 1 THR A 5 96.67 117.85 REMARK 500 1 ORN A 7 106.20 -14.39 REMARK 500 1 ASP A 8 -159.43 -132.77 REMARK 500 1 DSN A 12 -172.56 54.44 REMARK 500 1 LME A 13 -172.51 -68.50 REMARK 500 2 DSG A 3 155.19 -68.20 REMARK 500 2 THR A 5 89.87 84.61 REMARK 500 2 ORN A 7 113.59 6.12 REMARK 500 2 ASP A 8 166.03 93.50 REMARK 500 3 THR A 5 82.26 91.23 REMARK 500 3 ORN A 7 -93.20 15.99 REMARK 500 3 LME A 13 -173.23 62.28 REMARK 500 4 DSG A 3 81.67 -10.65 REMARK 500 4 THR A 5 68.73 89.02 REMARK 500 4 ORN A 7 -137.64 16.35 REMARK 500 4 ASP A 10 -71.38 -56.79 REMARK 500 5 DSG A 3 172.13 -103.23 REMARK 500 5 THR A 5 99.27 122.95 REMARK 500 5 ORN A 7 121.64 -1.57 REMARK 500 5 ASP A 8 -163.14 92.89 REMARK 500 6 DSG A 3 86.81 95.87 REMARK 500 6 THR A 5 86.91 97.66 REMARK 500 6 ORN A 7 94.15 -58.72 REMARK 500 6 DSN A 12 81.22 138.08 REMARK 500 7 DSG A 3 -102.70 -102.08 REMARK 500 7 THR A 5 97.49 123.93 REMARK 500 7 ASP A 8 167.40 95.85 REMARK 500 7 DSN A 12 121.43 121.37 REMARK 500 8 THR A 5 98.14 116.54 REMARK 500 8 ORN A 7 126.96 -4.57 REMARK 500 8 ASP A 8 124.58 100.66 REMARK 500 9 DSG A 3 100.09 104.72 REMARK 500 9 THR A 5 64.45 76.30 REMARK 500 9 ORN A 7 -89.70 -61.21 REMARK 500 9 DAL A 9 -123.00 -179.75 REMARK 500 9 DSN A 12 93.12 147.56 REMARK 500 9 LME A 13 161.89 85.50 REMARK 500 10 DSG A 3 167.23 -123.90 REMARK 500 10 THR A 5 98.13 97.75 REMARK 500 10 ORN A 7 -78.32 -23.01 REMARK 500 10 ASP A 10 -21.98 -173.56 REMARK 500 10 DSN A 12 111.06 117.02 REMARK 500 11 DSG A 3 177.95 -98.09 REMARK 500 11 THR A 5 95.24 84.43 REMARK 500 12 THR A 5 74.83 130.15 REMARK 500 12 ASP A 8 -158.20 -93.31 REMARK 500 13 DSG A 3 60.50 -123.67 REMARK 500 13 THR A 5 102.73 136.00 REMARK 500 REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS. 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 DSN A 12 LME A 13 2 -149.93 REMARK 500 TRP A 2 DSG A 3 4 143.88 REMARK 500 DSN A 12 LME A 13 4 -147.82 REMARK 500 TRP A 2 DSG A 3 5 -144.00 REMARK 500 DSN A 12 LME A 13 6 -30.20 REMARK 500 DSN A 12 LME A 13 8 -31.19 REMARK 500 DSN A 12 LME A 13 9 147.64 REMARK 500 DSN A 12 LME A 13 10 30.59 REMARK 500 TRP A 2 DSG A 3 11 -147.98 REMARK 500 DSN A 12 LME A 13 12 -148.93 REMARK 500 DSN A 12 LME A 13 13 32.51 REMARK 500 DSN A 12 LME A 13 14 -30.34 REMARK 500 DSN A 12 LME A 13 16 148.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XT7 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE ANTIBIOTIC DAPTOMYCIN REMARK 900 RELATED ID: 1T5M RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE CALCIUM-DEPENDENT ANTIBIOTIC DAPTOMYCIN DBREF 1T5N A 2 14 NOR NOR00001 NOR00001 2 14 SEQRES 1 A 13 TRP DSG ASP THR GLY ORN ASP DAL ASP GLY DSN LME KYN HET DSG A 3 14 HET ORN A 7 19 HET DAL A 9 10 HET DSN A 12 11 HET LME A 13 18 HET KYN A 14 24 HET DKA A 1 30 HETNAM DSG D-ASPARAGINE HETNAM ORN L-ORNITHINE HETNAM DAL D-ALANINE HETNAM DSN D-SERINE HETNAM LME (2S,3R)-2-AZANYL-3-METHYL-PENTANEDIOIC ACID HETNAM KYN (2S)-2-AMINO-4-(2-AMINOPHENYL)-4-OXOBUTANOIC ACID HETNAM DKA DECANOIC ACID HETSYN LME (3R)-3-METHYL-L-GLUTAMIC ACID HETSYN KYN L-KYNURENINE FORMUL 1 DSG C4 H8 N2 O3 FORMUL 1 ORN C5 H12 N2 O2 FORMUL 1 DAL C3 H7 N O2 FORMUL 1 DSN C3 H7 N O3 FORMUL 1 LME C6 H11 N O4 FORMUL 1 KYN C10 H12 N2 O3 FORMUL 2 DKA C10 H20 O2 LINK C1 DKA A 1 N TRP A 2 1555 1555 1.35 LINK C TRP A 2 N DSG A 3 1555 1555 1.35 LINK C DSG A 3 N ASP A 4 1555 1555 1.35 LINK OG1 THR A 5 C KYN A 14 1555 1555 1.39 LINK C GLY A 6 N ORN A 7 1555 1555 1.35 LINK C ORN A 7 N ASP A 8 1555 1555 1.35 LINK C ASP A 8 N DAL A 9 1555 1555 1.35 LINK C DAL A 9 N ASP A 10 1555 1555 1.35 LINK C GLY A 11 N DSN A 12 1555 1555 1.35 LINK C DSN A 12 N LME A 13 1555 1555 1.35 LINK C LME A 13 N KYN A 14 1555 1555 1.35 CISPEP 1 ORN A 7 ASP A 8 1 21.71 CISPEP 2 DSN A 12 LME A 13 1 -28.55 CISPEP 3 GLY A 11 DSN A 12 2 -24.71 CISPEP 4 GLY A 11 DSN A 12 3 -23.70 CISPEP 5 DSN A 12 LME A 13 3 -29.37 CISPEP 6 GLY A 11 DSN A 12 6 23.75 CISPEP 7 DSG A 3 ASP A 4 7 -29.17 CISPEP 8 DSN A 12 LME A 13 7 -26.38 CISPEP 9 DSG A 3 ASP A 4 8 -21.35 CISPEP 10 ORN A 7 ASP A 8 12 25.02 CISPEP 11 GLY A 11 DSN A 12 16 28.61 CISPEP 12 DSN A 12 LME A 13 17 15.53 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