HEADER ANTIBIOTIC 27-AUG-10 2L2W TITLE THIOSTREPTON COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOSTREPTON; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALANINAMIDE, BRYAMYCIN, GARGON, THIACTIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AZUREUS; SOURCE 3 ORGANISM_TAXID: 146537 KEYWDS NATURAL ANTIBIOTIC, THIOPEPTIDE, ANTIBIOTIC, ANTIMICROBIAL, KEYWDS 2 ANTIBACTERIAL, THIAZOLE, THIAZOLINE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.R.A.JONKER,S.BAUMANN,A.WOLF,S.SCHOOF,F.HILLER,K.W.SCHULTE, AUTHOR 2 K.N.KIRSCHNER,H.SCHWALBE,H.-D.ARNDT REVDAT 2 08-MAY-13 2L2W 1 LINK VERSN REVDAT 1 02-FEB-11 2L2W 0 JRNL AUTH H.R.JONKER,S.BAUMANN,A.WOLF,S.SCHOOF,F.HILLER,K.W.SCHULTE, JRNL AUTH 2 K.N.KIRSCHNER,H.SCHWALBE,H.D.ARNDT JRNL TITL NMR STRUCTURES OF THIOSTREPTON DERIVATIVES FOR JRNL TITL 2 CHARACTERIZATION OF THE RIBOSOMAL BINDING SITE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 50 3308 2011 JRNL REFN ISSN 1433-7851 JRNL PMID 21365717 JRNL DOI 10.1002/ANIE.201003582 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L2W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-11. REMARK 100 THE RCSB ID CODE IS RCSB101888. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10 MM THIOSTREPTON, CHLOROFORM- REMARK 210 D/ETHANOL-D5 5:1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C TOCSY-HSQC; 2D 1H-13C REMARK 210 HMBC; 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 ROESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, SPARKY 3.113, CNS REMARK 210 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 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 THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES REMARK 400 CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A REMARK 400 NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO REMARK 400 ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING REMARK 400 THIAZOLES, THIAZOLINES AND OXAZOLES. REMARK 400 HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 THE THIOSTREPTON IS THIOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: THIOSTREPTON REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: Thiostrepton is a hetrocyclic thiopeptide belonging REMARK 400 to the thiocillin family, consisting of four REMARK 400 thiazole, one thiozoline and one piperideine rings. REMARK 400 A modified quinoline linked to main-chain residue 1 REMARK 400 and side-chain of residue 12. Post translational REMARK 400 maturation of thiazole and oxazole containing REMARK 400 antibiotics involves the enzymic condensation of a REMARK 400 Cys or Ser with the alpha-carbonyl of the preceding REMARK 400 amino acid to form a thioether or ether bond, then REMARK 400 dehydration to form a double bond with the alpha- REMARK 400 amino nitrogen. Thiazoline or oxazoline ring are REMARK 400 dehydrogenated to form thiazole or oxazole rings. REMARK 400 the pyridinyl involves the cross-linking of a Ser REMARK 400 and a Cys-Ser pair usually separated by 7 or 8 REMARK 400 residues along the peptide chain. The Ser residues REMARK 400 are dehydrated to didehydroalanines, then bonded REMARK 400 between their beta carbons. The alpha carbonyl of REMARK 400 the Cys condenses with alpha carbon of the first Ser REMARK 400 to form a pyridinyl ring. The ring may be mutiply REMARK 400 dehydrogenated to form a pyridine ring with loss of REMARK 400 the amino nitrogen of the first Ser. The amidation REMARK 400 of Ser-17 probably does not occur by the same REMARK 400 mechanism, oxidative cleavage of glycine, as in REMARK 400 eukaryotes. 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 2 124.19 -172.56 REMARK 500 1 SER A 5 90.44 73.30 REMARK 500 1 DCY A 9 -37.98 -145.32 REMARK 500 2 ALA A 2 119.19 -172.12 REMARK 500 2 SER A 5 89.15 72.56 REMARK 500 2 DCY A 9 -37.74 -145.26 REMARK 500 3 ALA A 2 128.02 -171.24 REMARK 500 3 SER A 5 90.21 72.90 REMARK 500 3 DCY A 9 -38.01 -144.35 REMARK 500 4 ALA A 2 123.88 -172.27 REMARK 500 4 SER A 5 90.82 73.73 REMARK 500 4 DCY A 9 -36.60 -145.27 REMARK 500 5 ALA A 2 126.44 -172.33 REMARK 500 5 SER A 5 90.22 72.25 REMARK 500 5 DCY A 9 -40.55 -143.92 REMARK 500 6 ALA A 2 121.89 -173.51 REMARK 500 6 SER A 5 89.90 71.63 REMARK 500 6 DCY A 9 -40.52 -144.50 REMARK 500 7 ALA A 2 122.14 -172.71 REMARK 500 7 SER A 5 90.56 73.00 REMARK 500 7 DCY A 9 -42.50 -144.83 REMARK 500 8 ALA A 2 125.15 -170.64 REMARK 500 8 SER A 5 90.24 73.72 REMARK 500 8 DCY A 9 -29.32 -145.34 REMARK 500 9 ALA A 2 121.04 -171.57 REMARK 500 9 SER A 5 89.07 71.95 REMARK 500 9 DCY A 9 -29.84 -144.94 REMARK 500 10 ALA A 2 118.58 -173.13 REMARK 500 10 SER A 5 89.16 71.39 REMARK 500 10 DCY A 9 -37.36 -144.22 REMARK 500 11 ALA A 2 126.72 -170.41 REMARK 500 11 SER A 5 89.91 73.40 REMARK 500 11 DCY A 9 -30.45 -145.07 REMARK 500 12 ALA A 2 119.08 -172.80 REMARK 500 12 SER A 5 90.34 72.33 REMARK 500 12 DCY A 9 -41.98 -144.43 REMARK 500 13 ALA A 2 123.29 -171.70 REMARK 500 13 SER A 5 89.09 72.13 REMARK 500 13 DCY A 9 -39.17 -144.07 REMARK 500 14 SER A 5 89.74 72.64 REMARK 500 14 DCY A 9 -38.47 -144.27 REMARK 500 15 ALA A 2 119.95 -172.86 REMARK 500 15 SER A 5 90.02 71.89 REMARK 500 15 DCY A 9 -36.98 -145.04 REMARK 500 16 ALA A 2 122.41 -171.74 REMARK 500 16 SER A 5 89.77 71.68 REMARK 500 16 DCY A 9 -43.05 -144.31 REMARK 500 17 ALA A 2 123.94 -171.06 REMARK 500 17 SER A 5 91.55 72.09 REMARK 500 17 DCY A 9 -41.77 -145.17 REMARK 500 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. 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 DCY A 9 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E9W RELATED DB: PDB REMARK 900 RELATED ID: 2JQ7 RELATED DB: PDB REMARK 900 RELATED ID: 2L2X RELATED DB: PDB REMARK 900 RELATED ID: 2L2Y RELATED DB: PDB REMARK 900 RELATED ID: 2L2Z RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 A MODIFIED QUINOLINE LINKED TO THE MAIN-CHAIN OF RESIDUE 1 AND THE REMARK 999 SIDE-CHAIN OF RESIDUE 12. DBREF 2L2W A 1 17 UNP P0C8P8 THCL_STRAJ 1 17 SEQADV 2L2W QUA A 0 UNP P0C8P8 SEE REMARK 999 SEQADV 2L2W NH2 A 18 UNP P0C8P8 AMIDATION SEQRES 1 A 19 QUA ILE ALA DHA ALA SER BB9 THR DBU DCY TS9 BB9 THR SEQRES 2 A 19 BB9 MH6 BB9 DHA DHA NH2 MODRES 2L2W DHA A 3 SER 2-AMINO-ACRYLIC ACID MODRES 2L2W BB9 A 6 CYS MODRES 2L2W DBU A 8 THR (2E)-2-AMINOBUT-2-ENOIC ACID MODRES 2L2W TS9 A 10 ILE MODRES 2L2W BB9 A 11 CYS MODRES 2L2W BB9 A 13 CYS MODRES 2L2W MH6 A 14 SER 3-HYDROXY-2-IMINOPROPANOIC ACID MODRES 2L2W BB9 A 15 CYS MODRES 2L2W DHA A 16 SER 2-AMINO-ACRYLIC ACID MODRES 2L2W DHA A 17 SER 2-AMINO-ACRYLIC ACID HET QUA A 0 27 HET DHA A 3 8 HET BB9 A 6 7 HET DBU A 8 10 HET DCY A 9 9 HET TS9 A 10 20 HET BB9 A 11 7 HET BB9 A 13 7 HET MH6 A 14 6 HET BB9 A 15 7 HET DHA A 16 8 HET DHA A 17 8 HET NH2 A 18 3 HETNAM QUA 8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID HETNAM DHA 2-AMINO-ACRYLIC ACID HETNAM BB9 (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID HETNAM DBU (2Z)-2-AMINOBUT-2-ENOIC ACID HETNAM DCY D-CYSTEINE HETNAM TS9 (2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC ACID HETNAM MH6 3-HYDROXY-2-IMINOPROPANOIC ACID HETNAM NH2 AMINO GROUP HETSYN DHA 2,3-DIDEHYDROALANINE HETSYN DBU Z-DEHYDROBUTYRINE FORMUL 1 QUA C12 H13 N O4 FORMUL 1 DHA 3(C3 H5 N O2) FORMUL 1 BB9 4(C3 H5 N O2 S) FORMUL 1 DBU C4 H7 N O2 FORMUL 1 DCY C3 H7 N O2 S FORMUL 1 TS9 C6 H13 N O4 FORMUL 1 MH6 C3 H5 N O3 FORMUL 1 NH2 H2 N LINK C ALA A 2 N DHA A 3 1555 1555 1.33 LINK C DHA A 3 N ALA A 4 1555 1555 1.33 LINK C DHA A 16 N DHA A 17 1555 1555 1.34 LINK C SER A 5 N BB9 A 6 1555 1555 1.30 LINK C BB9 A 6 N THR A 7 1555 1555 1.33 LINK C THR A 7 N DBU A 8 1555 1555 1.33 LINK C DBU A 8 N DCY A 9 1555 1555 1.31 LINK C DCY A 9 N TS9 A 10 1555 1555 1.33 LINK C TS9 A 10 N BB9 A 11 1555 1555 1.30 LINK C BB9 A 11 N THR A 12 1555 1555 1.33 LINK C THR A 12 N BB9 A 13 1555 1555 1.29 LINK C BB9 A 13 N MH6 A 14 1555 1555 1.47 LINK C MH6 A 14 N BB9 A 15 1555 1555 1.29 LINK C BB9 A 15 N DHA A 16 1555 1555 1.34 LINK C11 QUA A 0 OG1 THR A 12 1555 1555 1.33 LINK C7 QUA A 0 N ILE A 1 1555 1555 1.49 LINK CB SER A 5 CB MH6 A 14 1555 1555 1.53 LINK CA SER A 5 C BB9 A 13 1555 1555 1.57 LINK C TS9 A 10 SG BB9 A 11 1555 1555 1.72 LINK C MH6 A 14 SG BB9 A 15 1555 1555 1.72 LINK C THR A 12 SG BB9 A 13 1555 1555 1.72 LINK C SER A 5 SG BB9 A 6 1555 1555 1.72 LINK C DBU A 8 SG DCY A 9 1555 1555 1.73 LINK C DHA A 17 N NH2 A 18 1555 1555 1.33 SITE 1 AC1 4 THR A 7 DBU A 8 TS9 A 10 BB9 A 11 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 O12 QUA A 0 0.586 -1.178 -0.398 1.00 1.00 O HETATM 2 C11 QUA A 0 -0.558 -1.189 0.058 1.00 1.00 C HETATM 3 C2 QUA A 0 -1.744 -1.654 -0.729 1.00 1.00 C HETATM 4 N1 QUA A 0 -2.973 -1.668 -0.147 1.00 1.00 N HETATM 5 C3 QUA A 0 -1.512 -2.051 -2.040 1.00 1.00 C HETATM 6 C9 QUA A 0 -4.003 -2.100 -0.927 1.00 1.00 C HETATM 7 C4 QUA A 0 -2.585 -2.488 -2.815 1.00 1.00 C HETATM 8 C8 QUA A 0 -5.373 -2.112 -0.257 1.00 1.00 C HETATM 9 C10 QUA A 0 -3.865 -2.513 -2.243 1.00 1.00 C HETATM 10 O16 QUA A 0 -5.999 -0.833 -0.395 1.00 1.00 O HETATM 11 C7 QUA A 0 -6.306 -3.200 -0.861 1.00 1.00 C HETATM 12 C13 QUA A 0 -2.351 -2.929 -4.260 1.00 1.00 C HETATM 13 O15 QUA A 0 -1.129 -2.386 -4.774 1.00 1.00 O HETATM 14 C5 QUA A 0 -5.055 -2.954 -2.987 1.00 1.00 C HETATM 15 C14 QUA A 0 -2.296 -4.448 -4.341 1.00 1.00 C HETATM 16 C6 QUA A 0 -6.162 -3.265 -2.386 1.00 1.00 C HETATM 17 HC3 QUA A 0 -0.514 -2.020 -2.453 1.00 1.00 H HETATM 18 HC8 QUA A 0 -5.252 -2.322 0.796 1.00 1.00 H HETATM 19 H16 QUA A 0 -6.040 -0.594 -1.323 1.00 1.00 H HETATM 20 HC71 QUA A 0 -7.327 -2.965 -0.604 1.00 1.00 H HETATM 21 H13 QUA A 0 -3.166 -2.587 -4.879 1.00 1.00 H HETATM 22 H15 QUA A 0 -1.152 -2.397 -5.734 1.00 1.00 H HETATM 23 HC5 QUA A 0 -5.010 -3.017 -4.063 1.00 1.00 H HETATM 24 H141 QUA A 0 -3.220 -4.863 -3.965 1.00 1.00 H HETATM 25 H142 QUA A 0 -1.471 -4.810 -3.745 1.00 1.00 H HETATM 26 H143 QUA A 0 -2.158 -4.749 -5.368 1.00 1.00 H HETATM 27 HC6 QUA A 0 -7.008 -3.581 -2.979 1.00 1.00 H