HEADER DNA 16-SEP-04 1W86 TITLE SOLUTION STRUCTURE OF AN DSDNA:LNA TRIPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTRAMOLECULAR DSDNA-LNA TRIPLEX; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN COMPND 5 A8 AND T9; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: INTRAMOLECULAR DSDNA-LNA TRIPLEX; COMPND 8 CHAIN: B; COMPND 9 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN COMPND 10 T16 AND T17; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: INTRAMOLECULAR DSDNA-LNA TRIPLEX; COMPND 13 CHAIN: C; COMPND 14 OTHER_DETAILS: C18, C20 AND C22 (LNA NUCLEOTIDES) ARE COMPND 15 PROTONATED AT N3 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS DNA COMPLEX, LNA, DNA, TRIPLEX, NMR SPECTROSCOPY, STRUCTURE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.J.SORENSEN,J.T.NIELSEN,M.PETERSEN REVDAT 4 24-NOV-09 1W86 1 VERSN REVDAT 3 24-FEB-09 1W86 1 VERSN REVDAT 2 01-DEC-05 1W86 1 REMARK ATOM HETATM CONECT REVDAT 1 25-NOV-04 1W86 0 JRNL AUTH J.J.SORENSEN,J.T.NIELSEN,M.PETERSEN JRNL TITL SOLUTION STRUCTURE OF A DSDNA:LNA TRIPLEX JRNL REF NUCLEIC ACIDS RES. V. 32 6078 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 15550567 JRNL DOI 10.1093/NAR/GKH942 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 1W86 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-SEP-04. REMARK 100 THE PDBE ID CODE IS EBI-21072. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308.0 REMARK 210 PH : 5.1 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : 1.0 REMARK 210 SAMPLE CONTENTS : D2O OR 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY,COSY,TOCSY,NOESY- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 REMARK 210 SPECTROMETER MODEL : UNITYINOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : 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 : NULL REMARK 210 REMARK 210 REMARK: NONE 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 GENERATING THE BIOMOLECULE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 DG A 2 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 3 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT B 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC B 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT C 17 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DT C 19 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT C 21 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT C 21 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT C 23 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT C 23 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT C 24 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT C 24 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 2 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA A 3 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DT B 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT B 10 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC B 11 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT B 12 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT B 14 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT C 17 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT C 19 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DT C 21 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT C 21 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT C 23 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT C 23 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 DA A 3 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 474 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 DA A 8 0.07 SIDE CHAIN REMARK 500 1 DC B 15 0.06 SIDE CHAIN REMARK 500 3 DC B 15 0.12 SIDE CHAIN REMARK 500 3 DT C 21 0.07 SIDE CHAIN REMARK 500 4 DA A 8 0.05 SIDE CHAIN REMARK 500 5 DA A 1 0.05 SIDE CHAIN REMARK 500 5 DA A 8 0.06 SIDE CHAIN REMARK 500 5 DT C 17 0.07 SIDE CHAIN REMARK 500 6 DC B 15 0.07 SIDE CHAIN REMARK 500 6 DT C 17 0.06 SIDE CHAIN REMARK 500 7 DA A 8 0.06 SIDE CHAIN REMARK 500 7 DC B 15 0.12 SIDE CHAIN REMARK 500 7 DT B 16 0.06 SIDE CHAIN REMARK 500 7 DT C 21 0.06 SIDE CHAIN REMARK 500 8 DA A 5 0.05 SIDE CHAIN REMARK 500 8 DA A 8 0.05 SIDE CHAIN REMARK 500 9 DA A 5 0.07 SIDE CHAIN REMARK 500 9 DT C 17 0.08 SIDE CHAIN REMARK 500 10 DC B 15 0.07 SIDE CHAIN REMARK 500 10 DT C 17 0.06 SIDE CHAIN REMARK 500 11 DA A 8 0.05 SIDE CHAIN REMARK 500 11 DT C 21 0.06 SIDE CHAIN REMARK 500 12 DT C 17 0.08 SIDE CHAIN REMARK 500 12 DT C 21 0.07 SIDE CHAIN REMARK 500 13 DA A 1 0.06 SIDE CHAIN REMARK 500 13 DA A 8 0.06 SIDE CHAIN REMARK 500 13 DT B 9 0.06 SIDE CHAIN REMARK 500 14 DA A 1 0.06 SIDE CHAIN REMARK 500 14 DC B 11 0.08 SIDE CHAIN REMARK 500 14 DC B 15 0.06 SIDE CHAIN REMARK 500 17 DA A 8 0.06 SIDE CHAIN REMARK 500 17 DT B 9 0.06 SIDE CHAIN REMARK 500 18 DA A 8 0.06 SIDE CHAIN REMARK 500 19 DA A 5 0.06 SIDE CHAIN REMARK 500 19 DT C 17 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1W86 A 1 8 PDB 1W86 1W86 1 8 DBREF 1W86 B 9 16 PDB 1W86 1W86 9 16 DBREF 1W86 C 17 24 PDB 1W86 1W86 17 24 SEQRES 1 A 8 DA DG DA DG DA DG DA DA SEQRES 1 B 8 DT DT DC DT DC DT DC DT SEQRES 1 C 8 DT LCC DT LCC DT LCC DT DT MODRES 1W86 LCC C 18 C MODIFIED CYTOSINE NUCLEOTIDE MODRES 1W86 LCC C 20 C MODIFIED CYTOSINE NUCLEOTIDE MODRES 1W86 LCC C 22 C MODIFIED CYTOSINE NUCLEOTIDE HET LCC C 18 35 HET LCC C 20 35 HET LCC C 22 35 HETNAM LCC [(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN- HETNAM 2 LCC 1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL HETNAM 3 LCC DIHYDROGEN PHOSPHATE FORMUL 3 LCC 3(C11 H16 N3 O8 P) LINK O3' DT C 17 P LCC C 18 1555 1555 1.62 LINK O3' LCC C 18 P DT C 19 1555 1555 1.61 LINK O3' DT C 19 P LCC C 20 1555 1555 1.62 LINK O3' LCC C 20 P DT C 21 1555 1555 1.62 LINK O3' DT C 21 P LCC C 22 1555 1555 1.62 LINK O3' LCC C 22 P DT C 23 1555 1555 1.62 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