PDB Short entry for 1TOB HEADER RNA 12-DEC-96 1TOB TITLE SACCHARIDE-RNA RECOGNITION IN AN AMINOGLYCOSIDE ANTIBIOTIC-RNA APTAMER TITLE 2 COMPLEX, NMR, 7 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(GGCACGAGGUUUAGCUACACUCGUGCC)-3'); 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 RIBONUCLEIC ACID, RNA EXPDTA SOLUTION NMR NUMMDL 7 AUTHOR L.JIANG,A.K.SURI,R.FIALA,D.J.PATEL REVDAT 4 29-JUL-20 1TOB 1 COMPND REMARK HETNAM SITE REVDAT 4 2 1 ATOM REVDAT 3 24-JUN-20 1TOB 1 SOURCE REMARK DBREF LINK REVDAT 2 24-FEB-09 1TOB 1 VERSN REVDAT 1 16-JUN-97 1TOB 0 JRNL AUTH L.JIANG,A.K.SURI,R.FIALA,D.J.PATEL JRNL TITL SACCHARIDE-RNA RECOGNITION IN AN AMINOGLYCOSIDE JRNL TITL 2 ANTIBIOTIC-RNA APTAMER COMPLEX. JRNL REF CHEM.BIOL. V. 4 35 1997 JRNL REFN ISSN 1074-5521 JRNL PMID 9070426 JRNL DOI 10.1016/S1074-5521(97)90235-0 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: RESTRAINED MOLECULAR DYNAMICS. REMARK 4 REMARK 4 1TOB 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_1000176766. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL 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 : X-PLOR 3.1 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY (INCLUDING RESTRAINT REMARK 210 ENERGY TERM) REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 HO2' G A 6 OP1 A A 7 1.51 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 3 C A 15 N1 C A 15 C6 -0.038 REMARK 500 4 C A 15 N1 C A 15 C6 -0.042 REMARK 500 4 G A 23 C2' G A 23 C1' -0.056 REMARK 500 5 C A 15 N1 C A 15 C6 -0.056 REMARK 500 6 C A 15 N1 C A 15 C6 -0.054 REMARK 500 7 C A 15 N1 C A 15 C6 -0.046 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 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 2 C1' - O4' - C4' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 A A 4 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 C A 5 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 G A 6 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 G A 6 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 1 A A 7 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 A A 7 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 1 U A 11 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 U A 12 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 A A 13 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 14 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 14 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 C A 15 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 A A 17 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 C A 18 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C A 18 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 C A 20 O4' - C1' - N1 ANGL. DEV. = 9.0 DEGREES REMARK 500 1 U A 21 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 C A 22 C1' - O4' - C4' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 G A 23 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U A 24 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 C A 26 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 2 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 2 A A 4 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 C A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 U A 10 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 U A 12 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 A A 13 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 2 C A 15 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 A A 17 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 C A 18 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 2 C A 18 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 2 C A 20 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 U A 21 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES REMARK 500 2 G A 23 O4' - C1' - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 2 C A 26 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 G A 1 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 G A 2 C1' - O4' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 3 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 C A 5 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 A A 7 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 3 G A 8 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 3 G A 8 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 3 G A 9 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 164 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1TOB A 1 27 PDB 1TOB 1TOB 1 27 SEQRES 1 A 27 G G C A C G A G G U U U A SEQRES 2 A 27 G C U A C A C U C G U G C SEQRES 3 A 27 C HET TOA A 28 24 HET TOC A 30 26 HET TOB A 29 24 HETNAM TOA 3-AMMONIO-3-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM TOC 2,6-DIAMMONIO-2,3,6-TRIDEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM TOB 1,3-DIAMINO-5,6-DIHYDROXYCYCLOHEXANE FORMUL 2 TOA C6 H14 N O5 1+ FORMUL 3 TOC C6 H16 N2 O3 2+ FORMUL 4 TOB C6 H16 N2 O2 2+ LINK C1 TOA A 28 O6 TOB A 29 1555 1555 1.38 LINK C4 TOB A 29 O1 TOC A 30 1555 1555 1.44 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