HEADER DNA-RNA HYBRID 23-JUL-03 1OKF TITLE NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*ATLP*GP*AP*ATLP*AP*ATLP*GP*CP)-3'; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-L-LNA; COMPND 5 OTHER_DETAILS: ALPHA-L-LNA THYMINE MODIFICATIONS AT COMPND 6 POSITIONS 2,5 AND 7; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(*GP*CP*AP*UP*AP*UP*CP*AP*GP)-3'; COMPND 9 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA-RNA HYBRID, DNA/RNA HYBRID, ALPHA-L-LNA, LNA, RNA, NMR, KEYWDS 2 RNASE H, LOCKED NUCLEIC ACID EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.T.NIELSEN,P.C.STEIN,M.PETERSEN REVDAT 2 24-FEB-09 1OKF 1 VERSN REVDAT 1 09-OCT-03 1OKF 0 JRNL AUTH J.T.NIELSEN,P.C.STEIN,M.PETERSEN JRNL TITL NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID: JRNL TITL 2 STRUCTURAL IMPLICATIONS FOR RNASE H RECOGNITION JRNL REF NUCLEIC ACIDS RES. V. 31 5858 2003 JRNL REFN ISSN 0305-1048 JRNL PMID 14530434 JRNL DOI 10.1093/NAR/GKG800 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE REMARK 4 REMARK 4 1OKF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUL-03. REMARK 100 THE PDBE ID CODE IS EBI-13158. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 3 MM NUCLEIC ACID, 100 MM NACL, REMARK 210 10 MM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, AMBER REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 16 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 1H,1H-NOES FROM REMARK 210 NOESY AND WATERGATE NOESY EXPERIMENTS 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 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 1 DA A 4 C5' DA A 4 C4' 0.062 REMARK 500 2 DA A 4 C5' DA A 4 C4' 0.062 REMARK 500 3 DA A 4 C5' DA A 4 C4' 0.063 REMARK 500 4 DA A 4 C5' DA A 4 C4' 0.060 REMARK 500 5 DA A 4 C5' DA A 4 C4' 0.062 REMARK 500 6 DA A 4 C5' DA A 4 C4' 0.061 REMARK 500 7 DA A 4 C5' DA A 4 C4' 0.060 REMARK 500 8 DA A 4 C5' DA A 4 C4' 0.063 REMARK 500 9 DA A 4 C5' DA A 4 C4' 0.061 REMARK 500 10 DA A 4 C5' DA A 4 C4' 0.061 REMARK 500 11 DA A 4 C5' DA A 4 C4' 0.063 REMARK 500 12 DA A 4 C5' DA A 4 C4' 0.061 REMARK 500 13 DA A 4 C5' DA A 4 C4' 0.063 REMARK 500 14 DA A 4 C5' DA A 4 C4' 0.058 REMARK 500 15 DA A 4 C5' DA A 4 C4' 0.061 REMARK 500 16 DA A 4 C5' DA A 4 C4' 0.063 REMARK 500 17 DA A 4 C5' DA A 4 C4' 0.061 REMARK 500 18 DA A 4 C5' DA A 4 C4' 0.062 REMARK 500 19 DA A 4 C5' DA A 4 C4' 0.062 REMARK 500 20 DA A 4 C5' DA A 4 C4' 0.061 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG A 3 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 3 O3' - P - OP1 ANGL. DEV. = -16.9 DEGREES REMARK 500 1 DG A 3 O3' - P - OP2 ANGL. DEV. = -16.9 DEGREES REMARK 500 1 DG A 3 C3' - O3' - P ANGL. DEV. = -9.8 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 6 O4' - C1' - C2' ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 6 O3' - P - OP1 ANGL. DEV. = -26.1 DEGREES REMARK 500 1 DA A 6 O3' - P - OP2 ANGL. DEV. = -26.1 DEGREES REMARK 500 1 DA A 6 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DG A 8 C3' - C2' - C1' ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 8 O3' - P - O5' ANGL. DEV. = 14.1 DEGREES REMARK 500 1 DG A 8 O3' - P - OP1 ANGL. DEV. = -24.5 DEGREES REMARK 500 1 DG A 8 O3' - P - OP2 ANGL. DEV. = -24.5 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 C B 11 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 U B 15 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 C B 16 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 A B 17 C3' - C2' - C1' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 A B 17 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G B 18 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = -2.1 DEGREES REMARK 500 2 DG A 3 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 3 O3' - P - OP1 ANGL. DEV. = -15.6 DEGREES REMARK 500 2 DG A 3 O3' - P - OP2 ANGL. DEV. = -15.6 DEGREES REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = -10.6 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 6 O4' - C1' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DA A 6 O3' - P - OP1 ANGL. DEV. = -25.9 DEGREES REMARK 500 2 DA A 6 O3' - P - OP2 ANGL. DEV. = -25.9 DEGREES REMARK 500 2 DA A 6 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DG A 8 C3' - C2' - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DG A 8 O3' - P - O5' ANGL. DEV. = 14.7 DEGREES REMARK 500 2 DG A 8 O3' - P - OP1 ANGL. DEV. = -24.4 DEGREES REMARK 500 2 DG A 8 O3' - P - OP2 ANGL. DEV. = -24.4 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 C B 11 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 U B 15 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 2 C B 16 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 A B 17 C3' - C2' - C1' ANGL. DEV. = 5.5 DEGREES REMARK 500 2 G B 18 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 DG A 3 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DG A 3 O3' - P - OP1 ANGL. DEV. = -23.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 465 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 DC A 1 0.08 SIDE CHAIN REMARK 500 1 A B 17 0.11 SIDE CHAIN REMARK 500 2 DC A 1 0.08 SIDE CHAIN REMARK 500 2 A B 17 0.12 SIDE CHAIN REMARK 500 3 DC A 1 0.07 SIDE CHAIN REMARK 500 3 DC A 9 0.07 SIDE CHAIN REMARK 500 3 A B 17 0.10 SIDE CHAIN REMARK 500 4 DC A 1 0.07 SIDE CHAIN REMARK 500 4 A B 17 0.10 SIDE CHAIN REMARK 500 5 DC A 1 0.09 SIDE CHAIN REMARK 500 5 A B 17 0.12 SIDE CHAIN REMARK 500 6 DC A 1 0.07 SIDE CHAIN REMARK 500 6 A B 17 0.10 SIDE CHAIN REMARK 500 7 DC A 1 0.07 SIDE CHAIN REMARK 500 7 A B 17 0.10 SIDE CHAIN REMARK 500 8 DC A 1 0.08 SIDE CHAIN REMARK 500 8 A B 17 0.10 SIDE CHAIN REMARK 500 9 DC A 1 0.07 SIDE CHAIN REMARK 500 9 A B 17 0.11 SIDE CHAIN REMARK 500 10 DC A 1 0.07 SIDE CHAIN REMARK 500 10 A B 17 0.10 SIDE CHAIN REMARK 500 11 DC A 1 0.09 SIDE CHAIN REMARK 500 11 A B 17 0.11 SIDE CHAIN REMARK 500 11 G B 18 0.05 SIDE CHAIN REMARK 500 12 DC A 1 0.06 SIDE CHAIN REMARK 500 12 A B 17 0.11 SIDE CHAIN REMARK 500 13 DC A 1 0.08 SIDE CHAIN REMARK 500 13 A B 17 0.11 SIDE CHAIN REMARK 500 14 DC A 1 0.08 SIDE CHAIN REMARK 500 14 DG A 3 0.07 SIDE CHAIN REMARK 500 14 A B 17 0.12 SIDE CHAIN REMARK 500 15 DC A 1 0.07 SIDE CHAIN REMARK 500 15 A B 17 0.11 SIDE CHAIN REMARK 500 16 DC A 1 0.08 SIDE CHAIN REMARK 500 16 A B 17 0.11 SIDE CHAIN REMARK 500 17 DC A 1 0.08 SIDE CHAIN REMARK 500 17 A B 17 0.09 SIDE CHAIN REMARK 500 17 G B 18 0.06 SIDE CHAIN REMARK 500 18 DC A 1 0.09 SIDE CHAIN REMARK 500 18 A B 17 0.10 SIDE CHAIN REMARK 500 19 DC A 1 0.06 SIDE CHAIN REMARK 500 19 A B 17 0.11 SIDE CHAIN REMARK 500 20 DC A 1 0.08 SIDE CHAIN REMARK 500 20 DC A 9 0.06 SIDE CHAIN REMARK 500 20 A B 17 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1OKF A 1 9 PDB 1OKF 1OKF 1 9 DBREF 1OKF B 10 18 PDB 1OKF 1OKF 10 18 SEQRES 1 A 9 DC ATL DG DA ATL DA ATL DG DC SEQRES 1 B 9 G C A U A U C A G MODRES 1OKF ATL A 2 T MODIFIED THYMINE MODRES 1OKF ATL A 5 T MODIFIED THYMINE MODRES 1OKF ATL A 7 T MODIFIED THYMINE HET ATL A 2 34 HET ATL A 5 34 HET ATL A 7 34 HETNAM ATL [(1S,3R,4S,7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5- HETNAM 2 ATL DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL HETNAM 3 ATL DIHYDROGEN PHOSPHATE FORMUL 1 ATL 3(C11 H15 N2 O9 P) LINK O3' DC A 1 P ATL A 2 1555 1555 1.62 LINK O3' ATL A 2 P DG A 3 1555 1555 1.60 LINK O3' DA A 4 P ATL A 5 1555 1555 1.63 LINK O3' ATL A 5 P DA A 6 1555 1555 1.62 LINK O3' DA A 6 P ATL A 7 1555 1555 1.62 LINK O3' ATL A 7 P DG A 8 1555 1555 1.63 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