HEADER RNA 14-JAN-15 2MXS TITLE SOLUTION NMR-STRUCTURE OF THE NEOMYCIN SENSING RIBOSWITCH RNA BOUND TO TITLE 2 PAROMOMYCIN 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 KEYWDS RNA, RIBOSWITCH, AMINOGLYCOSIDE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.SCHMIDTKE,E.DUCHARDT-FERNER,O.OHLENSCHLAEGER,D.GOTTSTEIN,J.WOHNERT REVDAT 4 01-MAY-24 2MXS 1 REMARK HETSYN REVDAT 3 03-FEB-16 2MXS 1 JRNL REVDAT 2 13-JAN-16 2MXS 1 JRNL REVDAT 1 09-DEC-15 2MXS 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, CYANA 2.1, OPALP REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA), LUGINBUHL, GUNTERT, BILLETER AND REMARK 3 WUTHRICH (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000104177. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.64 MM RNA (27-MER), 0.64 MM REMARK 210 PAROMOMYCIN, 90% H2O/10% D2O; REMARK 210 0.89 MM 13C; 15N RNA (27-MER), REMARK 210 0.89 MM PAROMOMYCIN, 90% H2O/10% REMARK 210 D2O; 0.89 MM 13C; 15N RNA (27- REMARK 210 MER), 0.89 MM PAROMOMYCIN, 100% REMARK 210 D2O; 0.62 MM G-]13C; 15N] RNA REMARK 210 (27-MER), 0.62 MM PAROMOMYCIN, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HNCO; 2D 1H-15N REMARK 210 H56C56C4N3H; 2D 1H-15N HSQC NH2 REMARK 210 ONLY; 2D 1H-13C HSQC AROMATIC; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 3D 1H- REMARK 210 13C NOESY-HSQC ALIPHATIC; 3D 1H- REMARK 210 13C NOESY-HMQC AROMATIC; 3D HCCH- REMARK 210 COSY; 3D HCCH-TOCSY; 2D 1H-15N REMARK 210 LRHSQC; 2D DQF-COSY; 2D 1H-31P REMARK 210 HCP; 3D HCCH-TOCSY-E.COSY; 2D REMARK 210 13C FILTER NOESY; 2D 13C FILTER REMARK 210 TOCSY; 2D QUANT 31P COUPLED 1H, REMARK 210 13C HSQC; 2D QUANT 31P COUPLED REMARK 210 1H-13C HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 900 REMARK 210 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, SPARKY, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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 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 DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 C A 11 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U A 13 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 U A 18 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 G A 20 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 U A 21 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 C A 3 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 U A 4 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 U A 8 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 U A 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 A A 16 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 20 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 U A 21 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 2 A A 24 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 G A 20 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 U A 21 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 3 C A 23 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 A A 24 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 4 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 C A 11 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 4 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 4 U A 13 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 U A 15 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 4 U A 21 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 4 A A 24 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 G A 9 N3 - C2 - N2 ANGL. DEV. = -4.8 DEGREES REMARK 500 5 C A 11 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 5 C A 12 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 5 U A 13 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 5 U A 21 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 C A 23 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 6 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 6 C A 6 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 6 U A 7 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 195 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 0.07 SIDE CHAIN REMARK 500 1 U A 10 0.08 SIDE CHAIN REMARK 500 1 U A 18 0.06 SIDE CHAIN REMARK 500 1 G A 19 0.07 SIDE CHAIN REMARK 500 1 C A 22 0.12 SIDE CHAIN REMARK 500 1 A A 24 0.10 SIDE CHAIN REMARK 500 1 G A 25 0.07 SIDE CHAIN REMARK 500 2 G A 2 0.06 SIDE CHAIN REMARK 500 2 U A 7 0.10 SIDE CHAIN REMARK 500 2 G A 9 0.12 SIDE CHAIN REMARK 500 2 U A 14 0.07 SIDE CHAIN REMARK 500 2 U A 15 0.06 SIDE CHAIN REMARK 500 2 U A 18 0.07 SIDE CHAIN REMARK 500 2 C A 22 0.09 SIDE CHAIN REMARK 500 2 U A 26 0.08 SIDE CHAIN REMARK 500 2 C A 27 0.08 SIDE CHAIN REMARK 500 3 G A 9 0.11 SIDE CHAIN REMARK 500 3 U A 14 0.07 SIDE CHAIN REMARK 500 3 A A 16 0.08 SIDE CHAIN REMARK 500 3 U A 18 0.11 SIDE CHAIN REMARK 500 3 G A 19 0.06 SIDE CHAIN REMARK 500 3 U A 21 0.10 SIDE CHAIN REMARK 500 3 C A 22 0.09 SIDE CHAIN REMARK 500 4 G A 1 0.06 SIDE CHAIN REMARK 500 4 U A 4 0.08 SIDE CHAIN REMARK 500 4 G A 5 0.07 SIDE CHAIN REMARK 500 4 U A 7 0.13 SIDE CHAIN REMARK 500 4 U A 10 0.16 SIDE CHAIN REMARK 500 4 U A 14 0.07 SIDE CHAIN REMARK 500 4 G A 19 0.09 SIDE CHAIN REMARK 500 4 U A 21 0.06 SIDE CHAIN REMARK 500 4 C A 22 0.13 SIDE CHAIN REMARK 500 4 U A 26 0.07 SIDE CHAIN REMARK 500 5 G A 1 0.10 SIDE CHAIN REMARK 500 5 G A 2 0.10 SIDE CHAIN REMARK 500 5 C A 11 0.07 SIDE CHAIN REMARK 500 5 U A 18 0.07 SIDE CHAIN REMARK 500 5 U A 21 0.09 SIDE CHAIN REMARK 500 5 C A 22 0.14 SIDE CHAIN REMARK 500 5 A A 24 0.07 SIDE CHAIN REMARK 500 5 U A 26 0.07 SIDE CHAIN REMARK 500 6 U A 4 0.06 SIDE CHAIN REMARK 500 6 C A 6 0.10 SIDE CHAIN REMARK 500 6 U A 7 0.13 SIDE CHAIN REMARK 500 6 U A 8 0.08 SIDE CHAIN REMARK 500 6 G A 9 0.12 SIDE CHAIN REMARK 500 6 G A 19 0.06 SIDE CHAIN REMARK 500 6 G A 25 0.06 SIDE CHAIN REMARK 500 7 U A 4 0.13 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 197 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 PAR A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KXM RELATED DB: PDB REMARK 900 RELATED ID: 25427 RELATED DB: BMRB DBREF 2MXS A 1 27 PDB 2MXS 2MXS 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 PAR A 101 92 HETNAM PAR PAROMOMYCIN HETSYN PAR PAROMOMYCIN I; AMMINOSIDIN; CATENULIN; CRESTOMYCIN; HETSYN 2 PAR MONOMYCIN A; NEOMYCIN E FORMUL 2 PAR C23 H45 N5 O14 SITE 1 AC1 13 U A 4 G A 5 C A 6 G A 9 SITE 2 AC1 13 U A 10 C A 11 C A 12 A A 17 SITE 3 AC1 13 U A 18 G A 19 G A 20 U A 21 SITE 4 AC1 13 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