HEADER ANTIBIOTIC 27-AUG-10 2L2X TITLE THIOSTREPTON, OXIDIZED AT CA-CB BOND OF RESIDUE 9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOSTREPTON; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-16; COMPND 5 SYNONYM: ALANINAMIDE, BRYAMYCIN, GARGON, THIACTIN; COMPND 6 MUTATION: YES 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 26-JUN-13 2L2X 1 JRNL VERSN REVDAT 1 02-FEB-11 2L2X 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 2L2X 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 RCSB101889. 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 (BB9, 9), REMARK 210 CHLOROFORM-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 MACROCYCLIC 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 THIOPEPTIDE THIOSTREPTON OXIDIZED AT CA-CB BOND OF RESIDUE 9 IS REMARK 400 THIOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: THIOPEPTIDE THIOSTREPTON OXIDIZED AT CA-CB BOND OF RESIDUE 9 REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: THIOSTREPTON IS A HETEROCYCLIC THIOPEPTIDE, REMARK 400 CONSISTING OF FOUR THIAZOLES ONE THIOZOLINE ONE REMARK 400 PIPERIDEINE RINGS. A MODIFIED QUINOLINE LINKED TO REMARK 400 MAIN-CHAIN RESIDUE 1 AND SIDE-CHAIN OF RESIDUE 12. REMARK 400 IN THIS ENTRY RESIDUE 9 WAS CHEMICALLY MODIFIED: THE REMARK 400 CA-CB BOND WAS OXIDIZED FROM SINGLE TO DOUBLE. REMARK 400 RESIDUE 17 (HET DHA) WAS DELETED. 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 SER A 5 84.00 65.56 REMARK 500 2 ALA A 2 112.35 -160.95 REMARK 500 2 SER A 5 84.59 65.30 REMARK 500 3 SER A 5 82.10 64.16 REMARK 500 4 SER A 5 84.98 66.59 REMARK 500 5 SER A 5 83.36 65.88 REMARK 500 5 TS9 A 10 -61.44 -93.41 REMARK 500 6 SER A 5 84.77 65.92 REMARK 500 7 SER A 5 85.78 66.35 REMARK 500 7 TS9 A 10 -61.82 -91.01 REMARK 500 8 SER A 5 84.92 66.28 REMARK 500 9 ALA A 2 110.76 -162.39 REMARK 500 9 SER A 5 84.32 65.85 REMARK 500 10 SER A 5 83.64 64.84 REMARK 500 11 SER A 5 84.06 64.57 REMARK 500 12 SER A 5 83.90 65.28 REMARK 500 13 SER A 5 83.21 66.13 REMARK 500 14 SER A 5 83.88 65.89 REMARK 500 15 SER A 5 84.32 65.01 REMARK 500 15 TS9 A 10 -60.09 -92.18 REMARK 500 16 SER A 5 86.20 66.43 REMARK 500 17 SER A 5 83.66 65.82 REMARK 500 18 SER A 5 84.08 64.62 REMARK 500 19 SER A 5 83.86 64.60 REMARK 500 20 ALA A 2 115.38 -160.30 REMARK 500 20 SER A 5 84.79 66.10 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 BB9 A 13 MH6 A 14 13 148.72 REMARK 500 REMARK 500 REMARK: NULL 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: 2L2W 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. THE RESIDUE 9 IS BB9. THE CA-CB BOND OF REMARK 999 THE RESIDUE DCY 9 OF THE THIOSTREPTON HAS BEEN CHEMICALLY MODIFIED. REMARK 999 IT HAS BEEN OXIDIZED FROM SINGLE TO DOUBLE. DBREF 2L2X A 1 16 UNP P0C8P8 THCL_STRAJ 1 16 SEQADV 2L2X QUA A 0 UNP P0C8P8 SEE REMARK 999 SEQADV 2L2X NH2 A 17 UNP P0C8P8 AMIDATION SEQRES 1 A 18 QUA ILE ALA DHA ALA SER BB9 THR DBU BB9 TS9 BB9 THR SEQRES 2 A 18 BB9 MH6 BB9 DHA NH2 MODRES 2L2X DHA A 3 SER 2-AMINO-ACRYLIC ACID MODRES 2L2X BB9 A 6 CYS MODRES 2L2X DBU A 8 THR (2E)-2-AMINOBUT-2-ENOIC ACID MODRES 2L2X BB9 A 9 CYS MODRES 2L2X TS9 A 10 ILE MODRES 2L2X BB9 A 11 CYS MODRES 2L2X BB9 A 13 CYS MODRES 2L2X MH6 A 14 SER 3-HYDROXY-2-IMINOPROPANOIC ACID MODRES 2L2X BB9 A 15 CYS MODRES 2L2X DHA A 16 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 BB9 A 9 7 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 NH2 A 17 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 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 2(C3 H5 N O2) FORMUL 1 BB9 5(C3 H5 N O2 S) FORMUL 1 DBU C4 H7 N O2 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 1.34 LINK C DHA A 3 N ALA A 4 1555 1555 1.33 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 BB9 A 9 1555 1555 1.29 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 MH6 A 14 N BB9 A 15 1555 1555 1.29 LINK C BB9 A 15 N DHA A 16 1555 1555 1.33 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 1.52 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 THR A 12 SG BB9 A 13 1555 1555 1.72 LINK C MH6 A 14 SG BB9 A 15 1555 1555 1.72 LINK C SER A 5 SG BB9 A 6 1555 1555 1.73 LINK C DBU A 8 SG BB9 A 9 1555 1555 1.72 LINK C BB9 A 9 N TS9 A 10 1555 1555 1.33 LINK C BB9 A 13 N MH6 A 14 1555 1555 1.47 LINK C DHA A 16 N NH2 A 17 1555 1555 1.33 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 1.321 -1.117 -0.331 1.00 1.00 O HETATM 2 C11 QUA A 0 0.170 -1.181 0.097 1.00 1.00 C HETATM 3 C2 QUA A 0 -0.993 -1.612 -0.739 1.00 1.00 C HETATM 4 N1 QUA A 0 -2.237 -1.616 -0.192 1.00 1.00 N HETATM 5 C3 QUA A 0 -0.729 -1.994 -2.048 1.00 1.00 C HETATM 6 C9 QUA A 0 -3.250 -2.021 -1.004 1.00 1.00 C HETATM 7 C4 QUA A 0 -1.787 -2.406 -2.858 1.00 1.00 C HETATM 8 C8 QUA A 0 -4.636 -2.016 -0.370 1.00 1.00 C HETATM 9 C10 QUA A 0 -3.084 -2.420 -2.321 1.00 1.00 C HETATM 10 O16 QUA A 0 -5.242 -0.728 -0.520 1.00 1.00 O HETATM 11 C7 QUA A 0 -5.564 -3.091 -0.999 1.00 1.00 C HETATM 12 C13 QUA A 0 -1.520 -2.830 -4.302 1.00 1.00 C HETATM 13 O15 QUA A 0 -0.303 -2.251 -4.792 1.00 1.00 O HETATM 14 C5 QUA A 0 -4.260 -2.843 -3.097 1.00 1.00 C HETATM 15 C14 QUA A 0 -1.423 -4.346 -4.393 1.00 1.00 C HETATM 16 C6 QUA A 0 -5.384 -3.148 -2.521 1.00 1.00 C HETATM 17 HC3 QUA A 0 0.281 -1.972 -2.433 1.00 1.00 H HETATM 18 HC8 QUA A 0 -4.545 -2.224 0.686 1.00 1.00 H HETATM 19 H16 QUA A 0 -5.126 -0.423 -1.424 1.00 1.00 H HETATM 20 HC71 QUA A 0 -6.587 -2.845 -0.764 1.00 1.00 H HETATM 21 H13 QUA A 0 -2.332 -2.504 -4.931 1.00 1.00 H HETATM 22 H15 QUA A 0 0.437 -2.564 -4.265 1.00 1.00 H HETATM 23 HC5 QUA A 0 -4.191 -2.902 -4.171 1.00 1.00 H HETATM 24 H141 QUA A 0 -2.333 -4.788 -4.014 1.00 1.00 H HETATM 25 H142 QUA A 0 -0.585 -4.689 -3.804 1.00 1.00 H HETATM 26 H143 QUA A 0 -1.283 -4.637 -5.422 1.00 1.00 H HETATM 27 HC6 QUA A 0 -6.219 -3.452 -3.135 1.00 1.00 H