HEADER DNA/RNA 30-JAN-03 1NTQ TITLE 5'(DCCUCCUU)3':3'(RAGGAGGAAA)5' COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*AP*AP*AP*GP*GP*AP*GP*GP*A)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*CP*UP*CP*CP*UP*U)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA, RNA, HYBRID, PROPYNYL, DNA-RNA COMPLEX EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR B.M.ZNOSKO,T.W.BARNES III,T.R.KRUGH,D.H.TURNER REVDAT 3 23-FEB-22 1NTQ 1 REMARK REVDAT 2 24-FEB-09 1NTQ 1 VERSN REVDAT 1 10-JUN-03 1NTQ 0 JRNL AUTH B.M.ZNOSKO,T.W.BARNES III,T.R.KRUGH,D.H.TURNER JRNL TITL NMR STUDIES OF DNA SINGLE STRANDS AND DNA:RNA HYBRIDS WITH JRNL TITL 2 AND WITHOUT 1-PROPYNYLATION AT C5 OF OLIGOPYRIMIDINES JRNL REF J.AM.CHEM.SOC. V. 125 6090 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 12785839 JRNL DOI 10.1021/JA021285D REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.W.BARNES III,D.H.TURNER REMARK 1 TITL LONG-RANGE COOPERATIVITY IN MOLECULAR RECOGNITION OF RNA BY REMARK 1 TITL 2 OLIGODEOXYNUCLEOTIDES WITH MULTIPLE C5-(1-PROPYNYL) REMARK 1 TITL 3 PYRIMIDINES REMARK 1 REF J.AM.CHEM.SOC. V. 123 4107 2001 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA003208T REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 5.2, DISCOVER 95.0 REMARK 3 AUTHORS : VARIAN (VNMR), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 140 INTERPROTON DISTANCE RESTRAINTS, 18 HYDROGEN BOND RESTRAINTS, REMARK 3 AND 104 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1NTQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018194. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 303 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 80 MM NACL; 80 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : ~1MM HYBRID, 80 MM NACL, 10 MM REMARK 210 PHOSPHATE BUFFER, 0.5 MM EDTA, REMARK 210 90% H2O, 10% D2O; ~2.5 MM HYBRID, REMARK 210 80 MM NACL, 10 MM PHOSPHATE, REMARK 210 0.5 MM EDTA, 99.996% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, DISCOVER 95.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 A A 2 N3 A A 2 C4 0.122 REMARK 500 A A 2 C4 A A 2 C5 0.078 REMARK 500 A A 2 N7 A A 2 C8 0.067 REMARK 500 A A 3 N3 A A 3 C4 0.120 REMARK 500 A A 3 C4 A A 3 C5 0.077 REMARK 500 A A 3 N7 A A 3 C8 0.068 REMARK 500 A A 4 N3 A A 4 C4 0.122 REMARK 500 A A 4 C4 A A 4 C5 0.077 REMARK 500 A A 4 N7 A A 4 C8 0.069 REMARK 500 G A 5 N1 G A 5 C2 0.094 REMARK 500 G A 5 N3 G A 5 C4 0.098 REMARK 500 G A 5 C4 G A 5 C5 0.058 REMARK 500 G A 5 C5 G A 5 C6 0.130 REMARK 500 G A 5 N7 G A 5 C8 0.070 REMARK 500 G A 6 N1 G A 6 C2 0.092 REMARK 500 G A 6 N3 G A 6 C4 0.095 REMARK 500 G A 6 C4 G A 6 C5 0.058 REMARK 500 G A 6 C5 G A 6 C6 0.132 REMARK 500 G A 6 N7 G A 6 C8 0.072 REMARK 500 A A 7 N3 A A 7 C4 0.122 REMARK 500 A A 7 C4 A A 7 C5 0.075 REMARK 500 A A 7 N7 A A 7 C8 0.066 REMARK 500 G A 8 N1 G A 8 C2 0.093 REMARK 500 G A 8 N3 G A 8 C4 0.096 REMARK 500 G A 8 C4 G A 8 C5 0.058 REMARK 500 G A 8 C5 G A 8 C6 0.132 REMARK 500 G A 8 N7 G A 8 C8 0.072 REMARK 500 G A 9 N1 G A 9 C2 0.093 REMARK 500 G A 9 N3 G A 9 C4 0.096 REMARK 500 G A 9 C4 G A 9 C5 0.057 REMARK 500 G A 9 C5 G A 9 C6 0.130 REMARK 500 G A 9 N7 G A 9 C8 0.071 REMARK 500 A A 10 N3 A A 10 C4 0.121 REMARK 500 A A 10 C4 A A 10 C5 0.075 REMARK 500 A A 10 N7 A A 10 C8 0.068 REMARK 500 DC B 1 C4 DC B 1 N4 0.072 REMARK 500 DC B 1 N1 DC B 1 C6 0.131 REMARK 500 DC B 1 C2 DC B 1 N3 0.117 REMARK 500 DC B 1 C4 DC B 1 C5 -0.056 REMARK 500 DC B 2 C4 DC B 2 N4 0.072 REMARK 500 DC B 2 N1 DC B 2 C6 0.130 REMARK 500 DC B 2 C2 DC B 2 N3 0.116 REMARK 500 DC B 2 C4 DC B 2 C5 -0.056 REMARK 500 DU B 3 N1 DU B 3 C6 0.118 REMARK 500 DU B 3 C4 DU B 3 C5 0.115 REMARK 500 DC B 4 C4 DC B 4 N4 0.071 REMARK 500 DC B 4 N1 DC B 4 C6 0.129 REMARK 500 DC B 4 C2 DC B 4 N3 0.117 REMARK 500 DC B 4 C4 DC B 4 C5 -0.056 REMARK 500 DC B 5 C4 DC B 5 N4 0.071 REMARK 500 REMARK 500 THIS ENTRY HAS 57 BOND DEVIATIONS. 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 A A 2 C2 - N3 - C4 ANGL. DEV. = 5.2 DEGREES REMARK 500 A A 2 N3 - C4 - C5 ANGL. DEV. = -9.4 DEGREES REMARK 500 A A 2 C5 - N7 - C8 ANGL. DEV. = -6.4 DEGREES REMARK 500 A A 2 N7 - C8 - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 A A 2 C8 - N9 - C4 ANGL. DEV. = -6.5 DEGREES REMARK 500 A A 2 N9 - C4 - C5 ANGL. DEV. = 2.4 DEGREES REMARK 500 A A 2 N3 - C4 - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 A A 3 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 A A 3 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES REMARK 500 A A 3 N3 - C4 - C5 ANGL. DEV. = -9.2 DEGREES REMARK 500 A A 3 C5 - N7 - C8 ANGL. DEV. = -6.6 DEGREES REMARK 500 A A 3 N7 - C8 - N9 ANGL. DEV. = 8.4 DEGREES REMARK 500 A A 3 C8 - N9 - C4 ANGL. DEV. = -6.0 DEGREES REMARK 500 A A 3 N3 - C4 - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 A A 4 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 A A 4 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES REMARK 500 A A 4 N3 - C4 - C5 ANGL. DEV. = -9.3 DEGREES REMARK 500 A A 4 C5 - N7 - C8 ANGL. DEV. = -6.4 DEGREES REMARK 500 A A 4 N7 - C8 - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 A A 4 C8 - N9 - C4 ANGL. DEV. = -6.1 DEGREES REMARK 500 A A 4 N3 - C4 - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 G A 5 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 G A 5 C2 - N3 - C4 ANGL. DEV. = 11.2 DEGREES REMARK 500 G A 5 N3 - C4 - C5 ANGL. DEV. = -10.9 DEGREES REMARK 500 G A 5 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 5 C4 - C5 - N7 ANGL. DEV. = 2.7 DEGREES REMARK 500 G A 5 C5 - N7 - C8 ANGL. DEV. = -7.2 DEGREES REMARK 500 G A 5 N7 - C8 - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 G A 5 C8 - N9 - C4 ANGL. DEV. = -6.9 DEGREES REMARK 500 G A 5 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 G A 5 N3 - C4 - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 G A 5 C6 - C5 - N7 ANGL. DEV. = -3.6 DEGREES REMARK 500 G A 5 C5 - C6 - O6 ANGL. DEV. = -5.0 DEGREES REMARK 500 G A 6 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 G A 6 C2 - N3 - C4 ANGL. DEV. = 11.2 DEGREES REMARK 500 G A 6 N3 - C4 - C5 ANGL. DEV. = -10.8 DEGREES REMARK 500 G A 6 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 G A 6 C4 - C5 - N7 ANGL. DEV. = 2.5 DEGREES REMARK 500 G A 6 C5 - N7 - C8 ANGL. DEV. = -7.1 DEGREES REMARK 500 G A 6 N7 - C8 - N9 ANGL. DEV. = 8.7 DEGREES REMARK 500 G A 6 C8 - N9 - C4 ANGL. DEV. = -6.9 DEGREES REMARK 500 G A 6 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 G A 6 N3 - C4 - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 G A 6 C5 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 A A 7 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 A A 7 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES REMARK 500 A A 7 N3 - C4 - C5 ANGL. DEV. = -9.3 DEGREES REMARK 500 A A 7 C5 - N7 - C8 ANGL. DEV. = -6.5 DEGREES REMARK 500 A A 7 N7 - C8 - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 A A 7 C8 - N9 - C4 ANGL. DEV. = -6.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 107 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 A A 2 0.08 SIDE CHAIN REMARK 500 G A 9 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NTS RELATED DB: PDB REMARK 900 DNA:RNA HYBRID WITH PROPYNYLATED BASES 1-7 IN DNA STRAND REMARK 900 RELATED ID: 1NTT RELATED DB: PDB REMARK 900 DNA:RNA HYBRID WITH PROPYNYLATED BASES 2-7 IN DNA STRAND DBREF 1NTQ A 2 10 PDB 1NTQ 1NTQ 2 10 DBREF 1NTQ B 1 7 PDB 1NTQ 1NTQ 1 7 SEQRES 1 A 9 A A A G G A G G A SEQRES 1 B 7 DC DC DU DC DC DU DU 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