HEADER DNA-RNA HYBRID 28-AUG-99 1CX5 TITLE ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*TP*T*(MMT)P*TP*GP*CP*GP*C); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: C3* OF THYMINE T 6 A BINDS DIRECTLY TO CO3* COMPND 6 OF MMT; O3* OF T 6 A IS MISSING; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(*GP*CP*GP*CP*AP*AP*AP*AP*CP*GP*CP*G); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS ANTISENSE, DNA/RNA HYBRID, NMR, MODIFIED BACKBONE LINKER, KEYWDS 2 DNA-RNA HYBRID EXPDTA SOLUTION NMR AUTHOR X.YANG,X.HAN,C.CROSS,Y.SANGHVI,X.GAO REVDAT 4 24-FEB-09 1CX5 1 VERSN REVDAT 3 01-APR-03 1CX5 1 JRNL REVDAT 2 07-APR-00 1CX5 1 JRNL REVDAT 1 14-SEP-99 1CX5 0 JRNL AUTH X.YANG,X.HAN,C.CROSS,S.BARE,Y.SANGHVI,X.GAO JRNL TITL NMR STRUCTURE OF AN ANTISENSE DNA.RNA HYBRID JRNL TITL 2 DUPLEX CONTAINING A 3'-CH(2)N(CH(3))-O-5' OR AN JRNL TITL 3 MMI BACKBONE LINKER. JRNL REF BIOCHEMISTRY V. 38 12586 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10504227 JRNL DOI 10.1021/BI990456X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CX5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-99. REMARK 100 THE RCSB ID CODE IS RCSB009601. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MM HYBRID DUPLEX IN 0.1 M REMARK 210 NACL, 10 MM SODIUM PHOSPHATE REMARK 210 AND 0.1 MM SODIUM EDTA. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR, FELIX 2.3/95/97, REMARK 210 MARDIGRAS, QUANTA 4/98 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 9 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED,BACK CALCULATED DATA REMARK 210 AGREE WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 RES CSSEQI ATOMS REMARK 470 DT A 6 O3' 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DC A 1 C2 - N3 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 2 C6 - N1 - C2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 3 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC A 3 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 3 N3 - C2 - O2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG A 4 C6 - N1 - C2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG A 4 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 4 N1 - C6 - O6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 5 C4' - C3' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 DT A 5 C3' - C2' - C1' ANGL. DEV. = 9.1 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT A 5 C2 - N3 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 5 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT A 5 N3 - C4 - O4 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT A 5 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 6 O4' - C4' - C3' ANGL. DEV. = 8.1 DEGREES REMARK 500 DT A 6 C4' - C3' - C2' ANGL. DEV. = -10.3 DEGREES REMARK 500 DT A 6 C3' - C2' - C1' ANGL. DEV. = 10.1 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT A 6 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 DT A 6 N1 - C2 - N3 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 6 C2 - N3 - C4 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT A 6 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 8 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 8 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 8 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG A 9 C5' - C4' - O4' ANGL. DEV. = 8.5 DEGREES REMARK 500 DG A 9 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A 9 N1 - C6 - O6 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 10 C2 - N3 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC A 10 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 11 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 11 N1 - C6 - O6 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 G B 101 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 G B 101 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 G B 101 N1 - C6 - O6 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 77 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 DC A 1 0.07 SIDE_CHAIN REMARK 500 DG A 2 0.08 SIDE_CHAIN REMARK 500 DG A 4 0.09 SIDE_CHAIN REMARK 500 DT A 5 0.13 SIDE_CHAIN REMARK 500 DT A 6 0.16 SIDE_CHAIN REMARK 500 DT A 8 0.13 SIDE_CHAIN REMARK 500 DG A 9 0.15 SIDE_CHAIN REMARK 500 DC A 10 0.08 SIDE_CHAIN REMARK 500 DG A 11 0.06 SIDE_CHAIN REMARK 500 C B 102 0.10 SIDE_CHAIN REMARK 500 G B 103 0.08 SIDE_CHAIN REMARK 500 A B 105 0.09 SIDE_CHAIN REMARK 500 C B 109 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1CX5 A 1 12 PDB 1CX5 1CX5 1 12 DBREF 1CX5 B 101 112 PDB 1CX5 1CX5 101 112 SEQRES 1 A 12 DC DG DC DG DT DT MMT DT DG DC DG DC SEQRES 1 B 12 G C G C A A A A C G C G MODRES 1CX5 MMT A 7 DT 5'-O-(DIMETHYLAMINO)-THYMIDINE HET MMT A 7 37 HETNAM MMT 5'-O-(DIMETHYLAMINO)-THYMIDINE FORMUL 1 MMT C12 H19 N3 O5 LINK C3' DT A 6 C3X MMT A 7 1555 1555 1.53 LINK O3' MMT A 7 P DT A 8 1555 1555 1.61 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 MASTER 155 0 1 0 0 0 0 6 0 0 0 2 END