0.037627 0.000000 0.000000 0.000000 0.037627 0.000000 0.000000 0.000000 0.036448 0.00000 0.00000 0.00000 Bond, C.S. Shaw, M.P. Alphey, M.S. Hunter, W.N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 26.577 26.577 27.436 C3 H7 N O2 89.093 y ALANINE L-peptide linking C3 H5 N O2 S 119.142 n (2Z)-2-amino-3-sulfanylprop-2-enoic acid peptide linking C4 H7 N O2 101.104 n (2Z)-2-AMINOBUT-2-ENOIC ACID Z-DEHYDROBUTYRINE peptide linking C3 H7 N O2 S 121.158 D-CYSTEINE D-peptide linking C3 H5 N O2 87.077 n 2-AMINO-ACRYLIC ACID 2,3-DIDEHYDROALANINE peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C3 H5 N O3 103.077 n 3-hydroxy-2-iminopropanoic acid peptide linking H2 N 16.023 AMINO GROUP non-polymer C12 H13 N O4 235.236 8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID non-polymer C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C6 H13 N O4 163.172 n (2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid L-peptide linking DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 57 755 10.1107/S0907444901003134 11320328 Structure of the Macrocycle Thiostrepton Solved Using the Anomalous Dispersive Contribution from Sulfur 2001 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 CCD MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.73 1.0 BM14 ESRF 0.73 SYNCHROTRON ESRF BEAMLINE BM14 1805.985 THIOSTREPTON 1 nat polymer 18.015 water 4 nat water ALANINAMIDE, BRYAMYCIN, THIACTIN no yes (QUA)IA(DHA)AS(BB9)T(DBU)(DCY)(TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2) XIASASCTTCICTCSCSSX A polypeptide(L) n n n n n n n n n n n n n n n n n n n CALBIOCHEM sample 146537 STREPTOMYCES AZUREUS 1 1.46 14.8 7.00 1ML 15.38MG/ML THIOSTREPTON IN CHLOROFORM_ISOAMYL ALCOHOL + 100 MICROL GLYCEROL + 200 MICROL ETHANOL. BATCH METHOD, pH 7.00 database_PDB_rev database_PDB_rev_record entity_poly pdbx_database_proc pdbx_database_status pdbx_seq_map_depositor_info struct_conn refine repository Initial release Atomic model Database references Derived calculations Structure summary Version format compliance Other Data collection Derived calculations Other Polymer sequence Data collection Refinement description 1 0 2001-03-23 1 1 2011-07-13 1 2 2012-11-30 2 0 2019-04-24 2 1 2019-05-22 _entity_poly.pdbx_seq_one_letter_code_can _pdbx_database_status.recvd_author_approval _pdbx_seq_map_depositor_info.one_letter_code _struct_conn.pdbx_leaving_atom_flag _refine.pdbx_ls_cross_valid_method CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-MGGDP COMPLEXED WITH THE THIOPEPTIDE GE2270A. SOLUTION STRUCTURE OF THIOPEPTIDE THIOSTREPTON BINDING TO L11 SUBSTRATE FROM 50S RIBOSOMAL RNA CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-GNP COMPLEXED WITH THIOPEPTIDE GE2270A. SOLUTION STRUCTURE OF THE COMPLEX OF THE THIOPEPTIDE THIOSTREPTON AND RIBOSOMAL L11-RNA CRYSTAL STRUCTURE OF NOSIHEPTIDE COMPLEXED WITH THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS CRYSTAL STRUCTURE OF RIBOSOMAL L11-RNA COMPLEXED WITH THE THIOPEPTIDE THIOSTREPTON PDBE Y PDBE 2000-10-27 REL HOH water THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING THIAZOLES, THIAZOLINES AND OXAZOLES. HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: THIOSTREPTON CHAIN: A COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 18 DESCRIPTION: THIOSTREPTON IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FOUR THIAZOLES ONE THIOZOLINE ONE PIPERIDEINE RINGS. A MODIFIED QUINOLINE LINKED TO MAIN-CHAIN RESIDUE 1 AND SIDE-CHAIN OF RESIDUE 12. THE OBSERVED C-TERMINAL AMINO GROUP NH2(18) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE Antibiotic Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes. THIOSTREPTON Thiopeptide HOH 2001 2 HOH HOH 2001 A HOH 2002 2 HOH HOH 2002 A HOH 2003 2 HOH HOH 2003 A HOH 2004 2 HOH HOH 2004 A QUA 0 n 1 QUA 0 A ILE 1 n 2 ILE 1 A ALA 2 n 3 ALA 2 A DHA 3 n 4 DHA 3 A ALA 4 n 5 ALA 4 A SER 5 n 6 SER 5 A BB9 6 n 7 BB9 6 A THR 7 n 8 THR 7 A DBU 8 n 9 DBU 8 A DCY 9 n 10 DCY 9 A TS9 10 n 11 TS9 10 A BB9 11 n 12 BB9 11 A THR 12 n 13 THR 12 A BB9 13 n 14 BB9 13 A MH6 14 n 15 MH6 14 A BB9 15 n 16 BB9 15 A DHA 16 n 17 DHA 16 A DHA 17 n 18 DHA 17 A NH2 18 n 19 NH2 18 A 0.1069 0.1122 0.1071 0.1124 0.1362 0.1423 755 825 9.8 9.8 7729 software_defined_assembly PISA 1 monomeric A DHA 3 2-AMINO-ACRYLIC ACID A DHA 4 SER A BB9 6 A BB9 7 CYS A DBU 8 (2Z)-2-AMINOBUT-2-ENOIC ACID A DBU 9 THR A TS9 10 A TS9 11 ILE A BB9 11 A BB9 12 CYS A BB9 13 A BB9 14 CYS A MH6 14 3-HYDROXY-2-IMINOPROPANOIC ACID A MH6 15 SER A BB9 15 A BB9 16 CYS A DHA 16 2-AMINO-ACRYLIC ACID A DHA 17 SER A DHA 17 2-AMINO-ACRYLIC ACID A DHA 18 SER 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A HOH 2001 B HOH 1 A HOH 2002 B HOH 1 A A C N BB9 MH6 13 14 0.139 0.023 1.336 1.475 Y 1 A SER 5 71.84 80.87 1 A DCY 9 -147.29 -14.74 1 A TS9 10 -107.46 -65.52 0.1423 0.1122 0.1124 1.02 50.00 1057 825 8391 1023 9.8 96.7 RANDOM 1 FREE R-VALUE 0.0 MOLECULAR REPLACEMENT SEE REFERENCE RESIDUE 16 RESTRAINED USING GEOMETRY DERIVED FROM CSD (SEE REFERENCE) ENGH AND HUBER MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 0 0.00 115.33 1.02 50.00 4 118 0 0 114 0.019 0.047 0.000 0.0001 0.000 0.000 0.051 0.007 0.037 0.000 1.020 50.000 1E9W 5232 0.03300 1 33.8000 4.300 96.7 0.15200 1.02 1.04 5.400 1 74.6 refinement SHELXL-97 data reduction DENZO data scaling SCALEPACK phasing SHELX THIOSTREPTON Structure of the macrocycle thiostrepton solved using the anomalous dispersive contribution from sulfur 1 N N 2 N N covale 1.329 one A QUA 0 A C11 QUA 1 1_555 A THR 12 A OG1 THR 13 1_555 covale 1.499 one A QUA 0 A C7 QUA 1 1_555 A ILE 1 A N ILE 2 1_555 covale 1.383 both A ALA 2 A C ALA 3 1_555 A DHA 3 A N DHA 4 1_555 covale 1.348 both A DHA 3 A C DHA 4 1_555 A ALA 4 A N ALA 5 1_555 covale 1.752 one A SER 5 A C SER 6 1_555 A BB9 6 A SG BB9 7 1_555 covale 1.575 one A SER 5 A CA SER 6 1_555 A BB9 13 A C BB9 14 1_555 covale 1.523 one A SER 5 A CB SER 6 1_555 A MH6 14 A CB MH6 15 1_555 covale 1.305 both A SER 5 A C SER 6 1_555 A BB9 6 A N BB9 7 1_555 covale 1.322 both A BB9 6 A C BB9 7 1_555 A THR 7 A N THR 8 1_555 covale 1.353 both A THR 7 A C THR 8 1_555 A DBU 8 A N DBU 9 1_555 covale 1.750 one A DBU 8 A C DBU 9 1_555 A DCY 9 A SG DCY 10 1_555 covale 1.293 both A DBU 8 A C DBU 9 1_555 A DCY 9 A N DCY 10 1_555 covale 1.328 both A DCY 9 A C DCY 10 1_555 A TS9 10 A N TS9 11 1_555 covale 1.750 one A TS9 10 A C TS9 11 1_555 A BB9 11 A SG BB9 12 1_555 covale 1.279 both A TS9 10 A C TS9 11 1_555 A BB9 11 A N BB9 12 1_555 covale 1.359 both A BB9 11 A C BB9 12 1_555 A THR 12 A N THR 13 1_555 covale 1.709 one A THR 12 A C THR 13 1_555 A BB9 13 A SG BB9 14 1_555 covale 1.292 both A THR 12 A C THR 13 1_555 A BB9 13 A N BB9 14 1_555 covale 1.475 both A BB9 13 A C BB9 14 1_555 A MH6 14 A N MH6 15 1_555 covale 1.650 one A MH6 14 A C MH6 15 1_555 A BB9 15 A SG BB9 16 1_555 covale 1.300 both A MH6 14 A C MH6 15 1_555 A BB9 15 A N BB9 16 1_555 covale 1.380 both A BB9 15 A C BB9 16 1_555 A DHA 16 A N DHA 17 1_555 covale 1.229 both A DHA 16 A C DHA 17 1_555 A DHA 17 A N DHA 18 1_555 covale 1.350 both A DHA 17 A C DHA 18 1_555 A NH2 18 A N NH2 19 1_555 ANTIBIOTIC ANTIBIOTIC, THIOPEPTIDE, ANTIBACTERIAL, THIAZOLE, THIAZOLINE, OXAZOLE, RIBOSOME, TRANSLATION INHIBITION THCL_STRAJ UNP 1 P0C8P8 1 17 1E9W 1 17 P0C8P8 A 1 2 18 BINDING SITE FOR RESIDUE QUA A 0 Software 15 BINDING SITE FOR RESIDUE NH2 A 18 Software 3 BINDING SITE FOR CHAIN A OF THIOSTREPTON Software 11 A ILE 1 A ILE 2 15 1_555 A ALA 2 A ALA 3 15 1_555 A DHA 3 A DHA 4 15 1_555 A DHA 3 A DHA 4 15 3_554 A ALA 4 A ALA 5 15 3_554 A ALA 4 A ALA 5 15 1_555 A SER 5 A SER 6 15 1_555 A BB9 6 A BB9 7 15 1_555 A THR 7 A THR 8 15 1_555 A TS9 10 A TS9 11 15 1_555 A BB9 11 A BB9 12 15 6_465 A THR 12 A THR 13 15 1_555 A BB9 13 A BB9 14 15 1_555 A NH2 18 A NH2 19 15 6_455 A HOH 2004 B HOH 15 1_555 A QUA 0 A QUA 1 3 6_555 A BB9 6 A BB9 7 3 7_555 A DHA 17 A DHA 18 3 1_555 A QUA 0 A QUA 1 11 1_555 A QUA 0 A QUA 1 11 4_455 A QUA 0 A QUA 1 11 6_565 A NH2 18 A NH2 19 11 1_555 A NH2 18 A NH2 19 11 7_555 A HOH 2001 B HOH 11 8_665 A HOH 2001 B HOH 11 1_555 A HOH 2002 B HOH 11 8_665 A HOH 2002 B HOH 11 1_555 A HOH 2003 B HOH 11 1_555 A HOH 2004 B HOH 11 1_555 96 P 43 21 2