HEADER STRUCTURAL PROTEIN/RNA/ANTIBIOTIC 21-NOV-06 2NYO OBSLTE 03-JUL-07 2NYO 2JQ7 TITLE MODEL FOR THIOSTREPTON BINDING TO THE RIBOSOMAL L11-RNA TITLE 2 REGION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBOSOMAL RNA; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: L11 BINDING DOMAIN, RESIDUES 1051-1108; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: THIOSTREPTON ANTIBIOTIC; COMPND 12 CHAIN: C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 GENE: RPLK; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: IN VITRO TRANSCRIBED RNA CONSTRUCT BASED ON SOURCE 12 SEQUENCE NATURALLY FOUND IN ESCHERICHIA COLI.; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: STREPTOMYCES AZUREUS; SOURCE 15 ORGANISM_COMMON: BACTERIA; SOURCE 16 OTHER_DETAILS: PURCHASED FROM SIGMA. KEYWDS L11, RNA, THIOSTREPTON, RIBOSOME, THIAZOLE, ANTIBIOTIC EXPDTA NMR, 10 STRUCTURES AUTHOR H.R.A.JONKER,S.ILIN,S.K.GRIMM,J.WOEHNERT,H.SCHWALBE REVDAT 3 03-JUL-07 2NYO 1 OBSLTE REVDAT 2 13-FEB-07 2NYO 1 JRNL REVDAT 1 06-FEB-07 2NYO 0 JRNL AUTH H.R.JONKER,S.ILIN,S.K.GRIMM,J.WOHNERT,H.SCHWALBE JRNL TITL L11 DOMAIN REARRANGEMENT UPON BINDING TO RNA AND JRNL TITL 2 THIOSTREPTON STUDIED BY NMR SPECTROSCOPY. JRNL REF NUCLEIC ACIDS RES. V. 35 441 2007 JRNL REFN ASTM NARHAD UK ISSN 0305-1048 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 2.0_DEVEL REMARK 3 AUTHORS : DOMINGUEZ ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FOR CHAIN A, THE INITIAL COORDINATES REMARK 3 ARE BASED ON PDB ENTRY 1MMS. OPTIMIZED USING RDCS. LEFT SEMI- REMARK 3 FLEXIBLE DURING DOCKING. FOR CHAIN B, INITIAL T. MARITIMA REMARK 3 COORDINATES ARE FROM PDB ENTRY 1MMS. LEFT SEMI-FLEXIBLE DURING REMARK 3 DOCKING. FOR CHAIN C, THE INITIAL COORDINATES ARE FROM PDB REMARK 3 ENTRY 1E9W. LEFT FLEXIBLE DURING DOCKING. THE DEVIATIONS IN REMARK 3 REMARK 500 ARE FOR AMINO ACIDS AND NUCLEIC ACIDS WHICH DO NOT REMARK 3 COMPLY WELL WITH THE ANTIBIOTIC IN THE CASE HERE. REMARK 4 REMARK 4 2NYO COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-18) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE RCSB ID CODE IS RCSB040466. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : 220 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.3 MM L11 U-15N,13C,2D, 0.3 REMARK 210 MM RNA, 0.3 MM THIOSTREPTON, REMARK 210 20 MM POTASSIUM PHOSPHATE REMARK 210 BUFFER PH 6.1 200 MM POTASSIUM REMARK 210 CHLORIDE, 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : IPAP(1H,15N)HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE, DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, XWINNMR 3.5, REMARK 210 NMRPIPE 2.5, SPARKY 3.112, CNS REMARK 210 1.1 REMARK 210 METHOD USED : THE MODEL WAS CALCULATED REMARK 210 USING HADDOCK. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE STRUCTURE WITH THE LOWEST REMARK 210 ENERGY WAS SELECTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE RDC DATA WAS USED TO DETERMINE THE RELATIVE DOMAIN REMARK 210 ORIENTATION OF THE L11 PROTEIN 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 1 MET A 1 REMARK 465 1 ALA A 2 REMARK 465 1 LYS A 3 REMARK 465 1 LYS A 4 REMARK 465 1 VAL A 5 REMARK 465 1 ALA A 6 REMARK 465 1 ALA A 7 REMARK 465 2 MET A 1 REMARK 465 2 ALA A 2 REMARK 465 2 LYS A 3 REMARK 465 2 LYS A 4 REMARK 465 2 VAL A 5 REMARK 465 2 ALA A 6 REMARK 465 2 ALA A 7 REMARK 465 3 MET A 1 REMARK 465 3 ALA A 2 REMARK 465 3 LYS A 3 REMARK 465 3 LYS A 4 REMARK 465 3 VAL A 5 REMARK 465 3 ALA A 6 REMARK 465 3 ALA A 7 REMARK 465 4 MET A 1 REMARK 465 4 ALA A 2 REMARK 465 4 LYS A 3 REMARK 465 4 LYS A 4 REMARK 465 4 VAL A 5 REMARK 465 4 ALA A 6 REMARK 465 4 ALA A 7 REMARK 465 5 MET A 1 REMARK 465 5 ALA A 2 REMARK 465 5 LYS A 3 REMARK 465 5 LYS A 4 REMARK 465 5 VAL A 5 REMARK 465 5 ALA A 6 REMARK 465 5 ALA A 7 REMARK 465 6 MET A 1 REMARK 465 6 ALA A 2 REMARK 465 6 LYS A 3 REMARK 465 6 LYS A 4 REMARK 465 6 VAL A 5 REMARK 465 6 ALA A 6 REMARK 465 6 ALA A 7 REMARK 465 7 MET A 1 REMARK 465 7 ALA A 2 REMARK 465 7 LYS A 3 REMARK 465 7 LYS A 4 REMARK 465 7 VAL A 5 REMARK 465 7 ALA A 6 REMARK 465 7 ALA A 7 REMARK 465 8 MET A 1 REMARK 465 8 ALA A 2 REMARK 465 8 LYS A 3 REMARK 465 8 LYS A 4 REMARK 465 8 VAL A 5 REMARK 465 8 ALA A 6 REMARK 465 8 ALA A 7 REMARK 465 9 MET A 1 REMARK 465 9 ALA A 2 REMARK 465 9 LYS A 3 REMARK 465 9 LYS A 4 REMARK 465 9 VAL A 5 REMARK 465 9 ALA A 6 REMARK 465 9 ALA A 7 REMARK 465 10 MET A 1 REMARK 465 10 ALA A 2 REMARK 465 10 LYS A 3 REMARK 465 10 LYS A 4 REMARK 465 10 VAL A 5 REMARK 465 10 ALA A 6 REMARK 465 10 ALA A 7 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 REMARK 500 O7 TZO C 13 N DHA C 14 2.15 REMARK 500 O DHA C 14 N PYT C 15 2.19 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 ILE C 8 CG1 ILE C 8 CD1 0.099 REMARK 500 1 ALA C 9 CA ALA C 9 CB 0.030 REMARK 500 1 ALA C 9 CA ALA C 9 C 0.076 REMARK 500 1 ALA C 9 C ALA C 9 O -0.050 REMARK 500 1 ILE C 8 C ALA C 9 N 0.040 REMARK 500 1 ALA C 9 C DHA C 10 N 0.060 REMARK 500 1 ALA C 11 CA ALA C 11 CB -0.031 REMARK 500 2 ILE C 8 CG1 ILE C 8 CD1 0.100 REMARK 500 2 ALA C 9 N ALA C 9 CA -0.032 REMARK 500 2 ALA C 9 CA ALA C 9 CB 0.032 REMARK 500 2 ALA C 9 CA ALA C 9 C 0.066 REMARK 500 2 ALA C 9 C ALA C 9 O -0.048 REMARK 500 2 ILE C 8 C ALA C 9 N 0.039 REMARK 500 2 ALA C 9 C DHA C 10 N 0.055 REMARK 500 2 ALA C 11 CA ALA C 11 CB -0.032 REMARK 500 3 ILE C 8 CG1 ILE C 8 CD1 0.100 REMARK 500 3 ALA C 9 CA ALA C 9 CB 0.032 REMARK 500 3 ALA C 9 CA ALA C 9 C 0.067 REMARK 500 3 ALA C 9 C ALA C 9 O -0.050 REMARK 500 3 ILE C 8 C ALA C 9 N 0.046 REMARK 500 3 ALA C 9 C DHA C 10 N 0.061 REMARK 500 3 ALA C 11 CA ALA C 11 CB -0.033 REMARK 500 4 ILE C 8 CG1 ILE C 8 CD1 0.100 REMARK 500 4 ALA C 9 CA ALA C 9 CB 0.035 REMARK 500 4 ALA C 9 CA ALA C 9 C 0.071 REMARK 500 4 ALA C 9 C ALA C 9 O -0.048 REMARK 500 4 ILE C 8 C ALA C 9 N 0.042 REMARK 500 4 ALA C 9 C DHA C 10 N 0.060 REMARK 500 4 ALA C 11 CA ALA C 11 CB -0.033 REMARK 500 5 ILE C 8 CG1 ILE C 8 CD1 0.100 REMARK 500 5 ALA C 9 CA ALA C 9 CB 0.031 REMARK 500 5 ALA C 9 CA ALA C 9 C 0.070 REMARK 500 5 ALA C 9 C ALA C 9 O -0.048 REMARK 500 5 ILE C 8 C ALA C 9 N 0.045 REMARK 500 5 ALA C 9 C DHA C 10 N 0.060 REMARK 500 5 ALA C 11 CA ALA C 11 CB -0.032 REMARK 500 6 ILE C 8 CG1 ILE C 8 CD1 0.100 REMARK 500 6 ALA C 9 CA ALA C 9 CB 0.035 REMARK 500 6 ALA C 9 CA ALA C 9 C 0.068 REMARK 500 6 ALA C 9 C ALA C 9 O -0.052 REMARK 500 6 ILE C 8 C ALA C 9 N 0.041 REMARK 500 6 ALA C 9 C DHA C 10 N 0.056 REMARK 500 6 ALA C 11 CA ALA C 11 CB -0.032 REMARK 500 7 ILE C 8 CG1 ILE C 8 CD1 0.099 REMARK 500 7 ALA C 9 CA ALA C 9 CB 0.032 REMARK 500 7 ALA C 9 CA ALA C 9 C 0.067 REMARK 500 7 ALA C 9 C ALA C 9 O -0.050 REMARK 500 7 ILE C 8 C ALA C 9 N 0.042 REMARK 500 7 ALA C 9 C DHA C 10 N 0.056 REMARK 500 7 ALA C 11 CA ALA C 11 CB -0.034 REMARK 500 8 ILE C 8 CG1 ILE C 8 CD1 0.100 REMARK 500 8 ALA C 9 CA ALA C 9 CB 0.035 REMARK 500 8 ALA C 9 CA ALA C 9 C 0.068 REMARK 500 8 ALA C 9 C ALA C 9 O -0.048 REMARK 500 8 ILE C 8 C ALA C 9 N 0.039 REMARK 500 8 ALA C 9 C DHA C 10 N 0.055 REMARK 500 8 ALA C 11 CA ALA C 11 CB -0.029 REMARK 500 9 ILE C 8 CG1 ILE C 8 CD1 0.101 REMARK 500 9 ALA C 9 CA ALA C 9 CB 0.035 REMARK 500 9 ALA C 9 CA ALA C 9 C 0.070 REMARK 500 9 ALA C 9 C ALA C 9 O -0.049 REMARK 500 9 ILE C 8 C ALA C 9 N 0.044 REMARK 500 9 ALA C 9 C DHA C 10 N 0.058 REMARK 500 9 ALA C 11 CA ALA C 11 CB -0.031 REMARK 500 10 ILE C 8 CG1 ILE C 8 CD1 0.099 REMARK 500 10 ALA C 9 CA ALA C 9 CB 0.034 REMARK 500 10 ALA C 9 CA ALA C 9 C 0.066 REMARK 500 10 ALA C 9 C ALA C 9 O -0.046 REMARK 500 10 ILE C 8 C ALA C 9 N 0.043 REMARK 500 10 ALA C 9 C DHA C 10 N 0.057 REMARK 500 10 ALA C 11 CA ALA C 11 CB -0.031 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ALA C 9 CB - CA - C ANGL. DEV. = -6.3 DEGREES REMARK 500 1 ALA C 9 N - CA - C ANGL. DEV. = -4.9 DEGREES REMARK 500 2 ALA C 9 CB - CA - C ANGL. DEV. = -5.8 DEGREES REMARK 500 2 ALA C 9 N - CA - C ANGL. DEV. = -7.0 DEGREES REMARK 500 2 ALA C 9 CA - C - N ANGL. DEV. = -5.5 DEGREES REMARK 500 2 ALA C 11 N - CA - C ANGL. DEV. = -4.9 DEGREES REMARK 500 3 ALA C 9 CB - CA - C ANGL. DEV. = -6.3 DEGREES REMARK 500 3 ALA C 9 N - CA - C ANGL. DEV. = -6.1 DEGREES REMARK 500 3 ALA C 9 CA - C - N ANGL. DEV. = -5.3 DEGREES REMARK 500 3 ALA C 11 N - CA - C ANGL. DEV. = -4.8 DEGREES REMARK 500 4 ALA C 9 CB - CA - C ANGL. DEV. = -6.0 DEGREES REMARK 500 4 ALA C 9 N - CA - C ANGL. DEV. = -5.8 DEGREES REMARK 500 4 ALA C 9 CA - C - N ANGL. DEV. = -5.1 DEGREES REMARK 500 4 ALA C 11 N - CA - C ANGL. DEV. = -5.5 DEGREES REMARK 500 5 ALA C 9 CB - CA - C ANGL. DEV. = -6.1 DEGREES REMARK 500 5 ALA C 9 N - CA - C ANGL. DEV. = -5.9 DEGREES REMARK 500 5 ALA C 9 CA - C - N ANGL. DEV. = -5.5 DEGREES REMARK 500 6 ALA C 9 CB - CA - C ANGL. DEV. = -5.8 DEGREES REMARK 500 6 ALA C 9 N - CA - C ANGL. DEV. = -6.8 DEGREES REMARK 500 6 ALA C 9 CA - C - N ANGL. DEV. = -5.2 DEGREES REMARK 500 7 ALA C 9 CB - CA - C ANGL. DEV. = -6.3 DEGREES REMARK 500 7 ALA C 9 N - CA - C ANGL. DEV. = -6.4 DEGREES REMARK 500 7 ALA C 9 CA - C - N ANGL. DEV. = -5.3 DEGREES REMARK 500 8 ALA C 9 CB - CA - C ANGL. DEV. = -5.4 DEGREES REMARK 500 8 ALA C 9 N - CA - C ANGL. DEV. = -6.7 DEGREES REMARK 500 9 ALA C 9 CB - CA - C ANGL. DEV. = -6.3 DEGREES REMARK 500 9 ALA C 9 N - CA - C ANGL. DEV. = -6.3 DEGREES REMARK 500 9 ALA C 9 CA - C - N ANGL. DEV. = -5.2 DEGREES REMARK 500 10 ALA C 9 CB - CA - C ANGL. DEV. = -6.2 DEGREES REMARK 500 10 ALA C 9 N - CA - C ANGL. DEV. = -6.3 DEGREES REMARK 500 10 ALA C 9 CA - C - N ANGL. DEV. = -5.5 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 3 GLU A 86 -67.35 73.98 REMARK 500 3 SER A 89 120.58 71.60 REMARK 500 3 LYS A 93 -41.70 73.72 REMARK 500 3 DHA C 10 -125.42 151.12 REMARK 500 4 THR A 101 135.52 74.56 REMARK 500 4 DHA C 10 138.47 128.27 REMARK 500 5 VAL A 33 127.65 73.30 REMARK 500 5 GLU A 86 -49.85 76.40 REMARK 500 5 ASN A 119 -74.29 68.81 REMARK 500 5 DHA C 10 -126.66 149.80 REMARK 500 6 VAL A 33 138.13 72.55 REMARK 500 6 GLU A 86 -93.11 74.74 REMARK 500 6 ASN A 119 -79.22 66.95 REMARK 500 6 ILE A 137 141.50 68.41 REMARK 500 7 ILE A 85 -59.96 74.40 REMARK 500 7 SER A 89 146.39 77.60 REMARK 500 7 DHA C 10 174.04 101.55 REMARK 500 8 GLU A 86 -106.70 71.17 REMARK 500 8 LYS A 93 -35.72 75.32 REMARK 500 9 GLU A 86 -60.39 72.56 REMARK 500 9 LYS A 93 -39.01 73.84 REMARK 500 9 DHA C 10 145.13 106.87 REMARK 500 10 GLU A 86 -66.89 72.65 REMARK 500 10 SER A 89 136.46 73.12 REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE ENTIRE CHAIN C (RESIDUES 1-15) IS THE ANTIBIOTIC REMARK 600 THIOSTREPTON. THE SEQUENCE IS TZO THR TZB TSI TZO XAA REMARK 600 QUA ILE ALA DHA ALA XBB TZO DHA PYT. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7308 RELATED DB: BMRB REMARK 900 BACKBONE ASSIGNMENT AND RDCS OF L11 IN COMPLEX WITH RNA AND REMARK 900 THIOSTREPTON REMARK 900 RELATED ID: 1MMS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RIBOSOMAL L11-RNA COMPLEX REMARK 900 RELATED ID: 1E9W RELATED DB: PDB REMARK 900 STRUCTURE OF THE MACROCYLCE THIOSTREPTON SOLVED USING THE REMARK 900 ANOMALOUS DISPERSIVE CONTRIBUTION FROM SULFUR REMARK 900 RELATED ID: 1OLN RELATED DB: PDB REMARK 900 MODEL FOR THIOSTREPTON ANTIBIOTIC BINDING TO L11 SUBSTRATE REMARK 900 FROM 50S RIBOSOMAL RNA DBREF 2NYO A 2 141 UNP P29395 RL11_THEMA 1 140 SEQADV 2NYO MET A 1 UNP P29395 INITIATING METHIONINE SEQRES 1 A 141 MET ALA LYS LYS VAL ALA ALA GLN ILE LYS LEU GLN LEU SEQRES 2 A 141 PRO ALA GLY LYS ALA THR PRO ALA PRO PRO VAL GLY PRO SEQRES 3 A 141 ALA LEU GLY GLN HIS GLY VAL ASN ILE MET GLU PHE CYS SEQRES 4 A 141 LYS ARG PHE ASN ALA GLU THR ALA ASP LYS ALA GLY MET SEQRES 5 A 141 ILE LEU PRO VAL VAL ILE THR VAL TYR GLU ASP LYS SER SEQRES 6 A 141 PHE THR PHE ILE ILE LYS THR PRO PRO ALA SER PHE LEU SEQRES 7 A 141 LEU LYS LYS ALA ALA GLY ILE GLU LYS GLY SER SER GLU SEQRES 8 A 141 PRO LYS ARG LYS ILE VAL GLY LYS VAL THR ARG LYS GLN SEQRES 9 A 141 ILE GLU GLU ILE ALA LYS THR LYS MET PRO ASP LEU ASN SEQRES 10 A 141 ALA ASN SER LEU GLU ALA ALA MET LYS ILE ILE GLU GLY SEQRES 11 A 141 THR ALA LYS SER MET GLY ILE GLU VAL VAL ASP SEQRES 1 B 58 G C U G G G A U G U U G G SEQRES 2 B 58 C U U A G A A G C A G C C SEQRES 3 B 58 A U C A U U U A A A G A G SEQRES 4 B 58 U G C G U A A C A G C U C SEQRES 5 B 58 A C C A G C SEQRES 1 C 4 ILE ALA DHA ALA MODRES 2NYO DHA C 10 ALA 2-AMINO-ACRYLIC ACID MODRES 2NYO DHA C 14 ALA 2-AMINO-ACRYLIC ACID HET DHA C 10 5 HET TZO C 1 7 HET THR C 2 7 HET TZB C 3 11 HET TSI C 4 8 HET TZO C 5 7 HET XAA C 6 10 HET TZO C 13 7 HET DHA C 14 5 HET PYT C 15 6 HET QUA C 7 16 HET XBB C 12 7 HETNAM DHA 2-AMINO-ACRYLIC ACID HETNAM TZO 1,3-THIAZOLE-4-CARBOXYLIC ACID HETNAM THR THREONINE HETNAM TZB (4S)-2-[(1E)-1-AMINOPROP-1-ENYL]-4,5-DIHYDRO-1,3- HETNAM 2 TZB THIAZOLE-4-CARBOXYLIC ACID HETNAM TSI (2S,3R)-1-AMINO-2-METHYLBUTANE-2,3-DIOL HETNAM XAA (1S,2S)-1-AMINO-1-(1,3-THIAZOL-2-YL)PROPAN-2-OL HETNAM PYT 2-AMINOPROP-2-ENAMIDE HETNAM QUA 8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC HETNAM 2 QUA ACID HETNAM XBB (3S)-2,3,4,5-TETRAHYDROPYRIDIN-3-AMINE HETSYN DHA 2,3-DIDEHYDROALANINE FORMUL 3 DHA 2(C3 H5 N O2) FORMUL 4 TZO 3(C4 H3 N O2 S) FORMUL 4 THR C4 H9 N O3 FORMUL 4 TZB C7 H10 N2 O2 S FORMUL 4 TSI C5 H13 N O2 FORMUL 5 XAA C6 H10 N2 O S FORMUL 6 PYT C3 H6 N2 O FORMUL 7 QUA C12 H13 N O4 FORMUL 8 XBB C5 H10 N2 HELIX 1 1 PRO A 20 GLN A 30 1 11 HELIX 2 2 ASN A 34 ASN A 43 1 10 HELIX 3 3 PRO A 74 GLY A 84 1 11 HELIX 4 4 THR A 101 LYS A 112 1 12 HELIX 5 5 SER A 120 SER A 134 1 15 SHEET 1 A 3 ILE A 9 PRO A 14 0 SHEET 2 A 3 ILE A 53 VAL A 60 -1 O VAL A 56 N LEU A 11 SHEET 3 A 3 PHE A 66 ILE A 70 -1 O THR A 67 N THR A 59 SHEET 1 B 2 GLY A 98 VAL A 100 0 SHEET 2 B 2 ILE A 137 VAL A 139 1 O GLU A 138 N GLY A 98 LINK C2 TZO C 1 C5 XBB C 12 LINK C6 TZO C 1 N THR C 2 LINK C THR C 2 N TZB C 3 LINK C6 TZB C 3 N1 TSI C 4 LINK C2 TSI C 4 C2 TZO C 5 LINK C6 TZO C 5 N7 XAA C 6 LINK C5 XAA C 6 C6 XBB C 12 LINK O10 XAA C 6 C11 QUA C 7 LINK C7 QUA C 7 N ILE C 8 LINK C ALA C 9 N DHA C 10 LINK C DHA C 10 N ALA C 11 LINK C ALA C 11 N7 XBB C 12 LINK C2 XBB C 12 C2 TZO C 13 LINK C6 TZO C 13 N DHA C 14 LINK C DHA C 14 N PYT C 15 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