HEADER RNA 17-JUN-98 2TOB TITLE SOLUTION STRUCTURE OF THE TOBRAMYCIN-RNA APTAMER COMPLEX, NMR, 13 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*AP*CP*UP*UP*GP*GP*UP*UP*UP*AP*GP*GP*UP*AP*AP*UP*GP*AP*GP*U)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS AMINOGLYCOSIDE-RNA RECOGNITION, TOBRAMYCIN, RNA EXPDTA SOLUTION NMR NUMMDL 13 AUTHOR L.JIANG,D.J.PATEL REVDAT 5 01-MAY-24 2TOB 1 HETSYN REVDAT 4 29-JUL-20 2TOB 1 COMPND REMARK HETNAM SITE REVDAT 4 2 1 ATOM REVDAT 3 24-JUN-20 2TOB 1 SOURCE REMARK DBREF LINK REVDAT 2 24-FEB-09 2TOB 1 VERSN REVDAT 1 22-JUN-99 2TOB 0 JRNL AUTH L.JIANG,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF THE TOBRAMYCIN-RNA APTAMER COMPLEX. JRNL REF NAT.STRUCT.BIOL. V. 5 769 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9731769 JRNL DOI 10.1038/1804 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2TOB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178692. 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 : 10MM NA(2)HPO(4) REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : D(2)O/H(2)O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; HMQCNULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VARIAN VNMR VNMR REMARK 210 METHOD USED : DISTANCE-RESTRAINED MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 13 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST NOE AND TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: D2O: 2D NOESY (50MS,120MS,200MS,300MS MIXING TIMES), PHASE REMARK 210 -SENSITIVE COSY, TOCSY, 1H-13C HSQC, 3D NOESY-HMQC (120MS, 300MS REMARK 210 MIXING TIMES), 3D HCCH-COSY, 3D HCCH-TOCSY (65MS), 2D HP REMARK 210 CORRELATION, C13 FILTERED NOESY 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 H3 U A 7 O6 G A 20 1.51 REMARK 500 OP2 G A 15 HN21 TOC A 102 1.56 REMARK 500 O6 G A 9 H61 A A 18 1.58 REMARK 500 HO2' A A 17 O4' A A 18 1.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 2TOB A 4 23 PDB 2TOB 2TOB 4 23 SEQRES 1 A 20 A C U U G G U U U A G G U SEQRES 2 A 20 A A U G A G U HET TOA A 100 24 HET TOC A 102 25 HET 2TB A 101 25 HETNAM TOA 3-AMMONIO-3-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM TOC 2,6-DIAMMONIO-2,3,6-TRIDEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM 2TB 1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE HETSYN TOA 3-DEOXY-3-AMINO GLUCOSE; 3-AMMONIO-3-DEOXY-ALPHA-D- HETSYN 2 TOA GLUCOSE; 3-AMMONIO-3-DEOXY-D-GLUCOSE; 3-AMMONIO-3- HETSYN 3 TOA DEOXY-GLUCOSE HETSYN TOC 2,3,6-TRIDEOXY-2,6-DIAMINO GLUCOSE; 2,6-DIAMMONIO-2,3, HETSYN 2 TOC 6-TRIDEOXY-ALPHA-D-GLUCOSE; 2,6-DIAMMONIO-2,3,6- HETSYN 3 TOC TRIDEOXY-D-GLUCOSE; 2,6-DIAMMONIO-2,3,6-TRIDEOXY- HETSYN 4 TOC GLUCOSE FORMUL 2 TOA C6 H14 N O5 1+ FORMUL 3 TOC C6 H16 N2 O3 2+ FORMUL 4 2TB C6 H16 N2 O3 2+ LINK C1 TOA A 100 O6 2TB A 101 1555 1555 1.40 LINK O4 2TB A 101 C1 TOC A 102 1555 1555 1.40 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