HEADER RNA 09-MAR-15 2N0J TITLE SOLUTION NMR STRUCTURE OF THE 27 NUCLEOTIDE ENGINEERED NEOMYCIN TITLE 2 SENSING RIBOSWITCH RNA-RIBOSTAMYCIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA_(27-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RIBOSWITCHES, RNA-LIGAND INTERACTION, AMINOGLYCOSIDES, RNA KEYWDS 2 RECOGNITION, RNA STRUCTURE, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.DUCHARDT-FERNER,S.R.GOTTSTEIN-SCHMIDTKE,J.E.WEIGAND, AUTHOR 2 O.E.OHLENSCHLAEGER,J.WURM,C.HAMMANN,B.SUESS,J.WOEHNERT REVDAT 1 03-FEB-16 2N0J 0 JRNL AUTH E.DUCHARDT-FERNER,S.R.GOTTSTEIN-SCHMIDTKE,J.E.WEIGAND, JRNL AUTH 2 O.OHLENSCHLAGER,J.P.WURM,C.HAMMANN,B.SUESS,J.WOHNERT JRNL TITL WHAT A DIFFERENCE AN OH MAKES: CONFORMATIONAL DYNAMICS AS JRNL TITL 2 THE BASIS FOR THE LIGAND SPECIFICITY OF THE NEOMYCIN-SENSING JRNL TITL 3 RIBOSWITCH. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 55 1527 2016 JRNL REFN ISSN 1433-7851 JRNL PMID 26661511 JRNL DOI 10.1002/ANIE.201507365 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.R.SCHMIDTKE,E.DUCHARDT-FERNER,J.E.WEIGAND,B.SUESS, REMARK 1 AUTH 2 J.WOHNERT REMARK 1 TITL NMR RESONANCE ASSIGNMENTS OF AN ENGINEERED NEOMYCIN-SENSING REMARK 1 TITL 2 RIBOSWITCH RNA BOUND TO RIBOSTAMYCIN AND TOBRAMYCIN. REMARK 1 REF BIOMOL.NMR ASSIGN. V. 4 115 2010 REMARK 1 REFN ISSN 1874-2718 REMARK 1 PMID 20306311 REMARK 1 DOI 10.1007/S12104-010-9223-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N0J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-15. REMARK 100 THE RCSB ID CODE IS RCSB104268. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 267; 283; 298 REMARK 210 PH : 6.2; 6.2; 6.2 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL REMARK 210 PRESSURE : NULL; NULL; NULL REMARK 210 SAMPLE CONTENTS : 0.8 MM RNA (27-MER), 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 0.8 MM [U-100% 15N] RNA (27- REMARK 210 MER), 0.9 MM RIBOSTAMYCIN, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1.1 MM [U-100% 13C; U-100% REMARK 210 15N] RNA (27-MER), 1.2 MM REMARK 210 RIBOSTAMYCIN, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 100% D2O; 1.1 MM [U- REMARK 210 13C; U-15N; U-2H] RNA (27-MER), REMARK 210 1.2 MM RIBOSTAMYCIN, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 100% D2O; 1.1 REMARK 210 MM [U-100% 13C; U-100% 15N] RNA REMARK 210 (27-MER), 1.2 MM RIBOSTAMYCIN, 25 REMARK 210 MM POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1.1 MM [U-13C; U-15N; U-2H] REMARK 210 RNA (27-MER), 1.2 MM REMARK 210 RIBOSTAMYCIN, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-15N HSQC; REMARK 210 3D 1H-15N NOESY; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D H(CCO)NH; 3D 1H-13C REMARK 210 NOESY; 2D 1H-1H TOCSY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 900 REMARK 210 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, CARA 1.8.4.2, REMARK 210 SPARKY, CYANA REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C A 6 O4' - C1' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C A 6 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 C A 6 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 U A 10 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 19 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 U A 21 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 C A 6 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 U A 18 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 U A 26 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 C A 6 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 3 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C A 12 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 3 U A 13 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 U A 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 U A 26 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 4 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 15 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 C A 23 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 C A 23 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 4 C A 27 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 5 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 5 C A 6 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 C A 6 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 5 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 U A 13 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 U A 14 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 U A 15 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 G A 20 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 5 C A 23 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 C A 27 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 C A 27 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 6 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 C A 6 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 6 C A 6 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 170 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 G A 1 0.06 SIDE CHAIN REMARK 500 1 G A 2 0.08 SIDE CHAIN REMARK 500 1 U A 4 0.15 SIDE CHAIN REMARK 500 1 G A 5 0.09 SIDE CHAIN REMARK 500 1 C A 6 0.06 SIDE CHAIN REMARK 500 1 U A 8 0.08 SIDE CHAIN REMARK 500 1 U A 10 0.10 SIDE CHAIN REMARK 500 1 U A 15 0.16 SIDE CHAIN REMARK 500 1 A A 17 0.06 SIDE CHAIN REMARK 500 1 C A 27 0.09 SIDE CHAIN REMARK 500 2 G A 2 0.08 SIDE CHAIN REMARK 500 2 U A 4 0.08 SIDE CHAIN REMARK 500 2 G A 5 0.10 SIDE CHAIN REMARK 500 2 C A 6 0.10 SIDE CHAIN REMARK 500 2 U A 8 0.13 SIDE CHAIN REMARK 500 2 G A 9 0.07 SIDE CHAIN REMARK 500 2 U A 10 0.15 SIDE CHAIN REMARK 500 2 U A 13 0.10 SIDE CHAIN REMARK 500 2 U A 14 0.07 SIDE CHAIN REMARK 500 2 A A 17 0.06 SIDE CHAIN REMARK 500 2 U A 26 0.11 SIDE CHAIN REMARK 500 3 G A 2 0.11 SIDE CHAIN REMARK 500 3 U A 4 0.06 SIDE CHAIN REMARK 500 3 G A 5 0.08 SIDE CHAIN REMARK 500 3 C A 6 0.11 SIDE CHAIN REMARK 500 3 U A 8 0.15 SIDE CHAIN REMARK 500 3 G A 9 0.08 SIDE CHAIN REMARK 500 3 U A 18 0.09 SIDE CHAIN REMARK 500 3 G A 19 0.05 SIDE CHAIN REMARK 500 4 G A 1 0.07 SIDE CHAIN REMARK 500 4 G A 2 0.08 SIDE CHAIN REMARK 500 4 C A 6 0.12 SIDE CHAIN REMARK 500 4 U A 10 0.14 SIDE CHAIN REMARK 500 4 C A 11 0.07 SIDE CHAIN REMARK 500 4 U A 15 0.08 SIDE CHAIN REMARK 500 4 U A 18 0.07 SIDE CHAIN REMARK 500 4 G A 20 0.08 SIDE CHAIN REMARK 500 4 C A 22 0.07 SIDE CHAIN REMARK 500 4 G A 25 0.08 SIDE CHAIN REMARK 500 4 C A 27 0.07 SIDE CHAIN REMARK 500 5 G A 2 0.11 SIDE CHAIN REMARK 500 5 C A 3 0.07 SIDE CHAIN REMARK 500 5 U A 4 0.10 SIDE CHAIN REMARK 500 5 G A 5 0.06 SIDE CHAIN REMARK 500 5 U A 8 0.15 SIDE CHAIN REMARK 500 5 U A 10 0.11 SIDE CHAIN REMARK 500 5 C A 11 0.07 SIDE CHAIN REMARK 500 5 U A 15 0.07 SIDE CHAIN REMARK 500 5 A A 17 0.06 SIDE CHAIN REMARK 500 5 G A 19 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 192 PLANE DEVIATIONS. 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 RIO A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16609 RELATED DB: BMRB REMARK 900 1H, 13C, 15N, 31P CHEMICAL SHIFT DEPOSITION REMARK 900 RELATED ID: 25526 RELATED DB: BMRB DBREF 2N0J A 1 27 PDB 2N0J 2N0J 1 27 SEQRES 1 A 27 G G C U G C U U G U C C U SEQRES 2 A 27 U U A A U G G U C C A G U SEQRES 3 A 27 C HET RIO A 101 69 HETNAM RIO RIBOSTAMYCIN HETSYN RIO 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY- HETSYN 2 RIO 5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY- HETSYN 3 RIO CYCLOHEXYLOXY]-TETRAHYDRO-PYRAN-3,4-DIOL; (1R,2R,3S, HETSYN 4 RIO 4R,6S)-4,6-DIAMINO-3-HYDROXY-2-(BETA-D- HETSYN 5 RIO RIBOFURANOSYLOXY)CYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY- HETSYN 6 RIO ALPHA-D-GLUCOPYRANOSIDE FORMUL 2 RIO C17 H34 N4 O10 SITE 1 AC1 11 U A 4 G A 5 G A 9 U A 10 SITE 2 AC1 11 C A 11 C A 12 A A 17 G A 19 SITE 3 AC1 11 G A 20 U A 21 C A 22 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