HEADER DNA 12-MAR-09 2WCN TITLE SOLUTION STRUCTURE OF AN LNA-MODIFIED QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*DGP*LCG*DGP*LCG*DTP*DTP*DTP COMPND 3 *DTP*DGP*LCG*DGP*LCG)-3'); COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: OXYTRICHA NOVA SEQUENCE; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: MODEL SYSTEM DERIVED FROM OXYTRICIA NOVA TELOMERE COMPND 8 SEQUNCE MODIFIED WITH LNA NUCLEOTIDES AT POSITION 2,4,10 AND 12. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: OXYTRICHA NOVA; SOURCE 4 ORGANISM_TAXID: 200597 KEYWDS LNA, QUADRUPLEX, FOLDING TOPOLOGY, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.T.NIELSEN,K.ARAR,M.PETERSEN REVDAT 2 15-MAY-24 2WCN 1 REMARK LINK REVDAT 1 24-NOV-09 2WCN 0 JRNL AUTH J.T.NIELSEN,K.ARAR,M.PETERSEN JRNL TITL SOLUTION STRUCTURE OF A LOCKED NUCLEIC ACID MODIFIED JRNL TITL 2 QUADRUPLEX: INTRODUCING THE V4 FOLDING TOPOLOGY. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 48 3099 2009 JRNL REFN ISSN 1433-7851 JRNL PMID 19308940 JRNL DOI 10.1002/ANIE.200806244 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.14 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2WCN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1290039034. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : H2O/D2O AND D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; HSQC 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 : X-PLOR 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 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 1 DG A 1 C8 DG A 1 N9 -0.046 REMARK 500 1 DT A 6 P DT A 6 O5' 0.073 REMARK 500 1 DT A 6 C5 DT A 6 C6 0.056 REMARK 500 1 DT A 6 C5 DT A 6 C7 0.069 REMARK 500 1 DG A 11 C5' DG A 11 C4' 0.043 REMARK 500 1 DG B 13 C8 DG B 13 N9 -0.047 REMARK 500 1 DT B 18 C5 DT B 18 C7 0.057 REMARK 500 2 DG A 1 C8 DG A 1 N9 -0.049 REMARK 500 2 DT A 6 P DT A 6 O5' 0.062 REMARK 500 2 DT A 6 C3' DT A 6 C2' -0.057 REMARK 500 2 DG A 11 C5' DG A 11 C4' 0.044 REMARK 500 2 DG B 13 C8 DG B 13 N9 -0.047 REMARK 500 2 DT B 18 P DT B 18 O5' 0.065 REMARK 500 2 DT B 18 C5' DT B 18 C4' 0.043 REMARK 500 2 DT B 18 C3' DT B 18 C2' -0.053 REMARK 500 2 DT B 18 C2' DT B 18 C1' -0.065 REMARK 500 2 DT B 20 P DT B 20 O5' 0.060 REMARK 500 2 DG B 23 C5' DG B 23 C4' 0.043 REMARK 500 3 DG A 1 C2' DG A 1 C1' -0.061 REMARK 500 3 DG A 1 C8 DG A 1 N9 -0.052 REMARK 500 3 DT A 5 C2' DT A 5 C1' -0.069 REMARK 500 3 DT A 5 C6 DT A 5 N1 -0.088 REMARK 500 3 DT A 6 C5 DT A 6 C7 0.041 REMARK 500 3 DG B 13 C8 DG B 13 N9 -0.050 REMARK 500 3 DT B 17 C2' DT B 17 C1' -0.078 REMARK 500 3 DT B 17 C6 DT B 17 N1 -0.088 REMARK 500 3 DT B 18 C5 DT B 18 C6 0.043 REMARK 500 3 DG B 23 C5' DG B 23 C4' 0.043 REMARK 500 4 DG A 1 C2' DG A 1 C1' -0.064 REMARK 500 4 DT A 5 O4' DT A 5 C4' -0.060 REMARK 500 4 DT A 6 P DT A 6 O5' 0.061 REMARK 500 4 DT A 6 C3' DT A 6 C2' -0.051 REMARK 500 4 DT A 6 C2' DT A 6 C1' -0.063 REMARK 500 4 DT A 8 O4' DT A 8 C4' -0.060 REMARK 500 4 DG A 9 O4' DG A 9 C4' -0.060 REMARK 500 4 DG B 13 C2' DG B 13 C1' -0.061 REMARK 500 4 DG B 13 C8 DG B 13 N9 -0.047 REMARK 500 4 DT B 18 C3' DT B 18 C2' -0.052 REMARK 500 4 DT B 18 C2' DT B 18 C1' -0.061 REMARK 500 4 DT B 20 O4' DT B 20 C4' -0.061 REMARK 500 5 DG A 1 C8 DG A 1 N9 -0.050 REMARK 500 5 DT A 5 C2' DT A 5 C1' -0.101 REMARK 500 5 DT A 5 C6 DT A 5 N1 -0.086 REMARK 500 5 DT A 6 C5 DT A 6 C7 0.045 REMARK 500 5 DG B 13 C8 DG B 13 N9 -0.044 REMARK 500 5 DT B 17 C3' DT B 17 C2' -0.052 REMARK 500 5 DT B 17 C2' DT B 17 C1' -0.142 REMARK 500 5 DT B 17 C6 DT B 17 N1 -0.088 REMARK 500 5 DT B 18 C5 DT B 18 C6 0.043 REMARK 500 5 DG B 23 C5' DG B 23 C4' 0.043 REMARK 500 REMARK 500 THIS ENTRY HAS 160 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 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 3 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT A 5 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 5 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C7 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -11.1 DEGREES REMARK 500 1 DT A 6 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DT A 6 C4 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 8 C4 - C5 - C7 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DG A 9 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG A 9 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG B 13 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG B 13 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG B 15 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DT B 17 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT B 17 O4' - C1' - C2' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DT B 17 C4 - C5 - C7 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -10.4 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DT B 19 O5' - C5' - C4' ANGL. DEV. = 18.4 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 20 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG B 21 C1' - O4' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 1 DG B 21 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 1 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DG A 1 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DG A 1 C4 - N9 - C1' ANGL. DEV. = 9.8 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DG A 3 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 2 DT A 5 O4' - C4' - C3' ANGL. DEV. = 11.6 DEGREES REMARK 500 2 DT A 5 C4' - C3' - C2' ANGL. DEV. = -9.2 DEGREES REMARK 500 2 DT A 5 C3' - C2' - C1' ANGL. DEV. = 13.0 DEGREES REMARK 500 2 DT A 5 C4 - C5 - C7 ANGL. DEV. = 9.9 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -9.7 DEGREES REMARK 500 2 DT A 5 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 2 DT A 6 O5' - C5' - C4' ANGL. DEV. = 17.3 DEGREES REMARK 500 2 DT A 6 C4' - C3' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1016 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 3 DT A 5 0.06 SIDE CHAIN REMARK 500 3 DT B 17 0.07 SIDE CHAIN REMARK 500 5 DT B 17 0.07 SIDE CHAIN REMARK 500 6 DT A 5 0.08 SIDE CHAIN REMARK 500 6 DT B 17 0.07 SIDE CHAIN REMARK 500 7 DT A 5 0.06 SIDE CHAIN REMARK 500 7 DT B 17 0.06 SIDE CHAIN REMARK 500 10 DT A 5 0.06 SIDE CHAIN REMARK 500 10 DT B 17 0.07 SIDE CHAIN REMARK 500 11 DT A 5 0.07 SIDE CHAIN REMARK 500 11 DT B 17 0.08 SIDE CHAIN REMARK 500 12 DT A 5 0.06 SIDE CHAIN REMARK 500 12 DT B 17 0.07 SIDE CHAIN REMARK 500 13 DT A 5 0.06 SIDE CHAIN REMARK 500 13 DT B 17 0.06 SIDE CHAIN REMARK 500 16 DT A 5 0.07 SIDE CHAIN REMARK 500 16 DT B 17 0.08 SIDE CHAIN REMARK 500 19 DT B 17 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2WCN A 1 12 PDB 2WCN 2WCN 1 12 DBREF 2WCN B 13 24 PDB 2WCN 2WCN 13 24 SEQRES 1 A 12 DG LCG DG LCG DT DT DT DT DG LCG DG LCG SEQRES 1 B 12 DG LCG DG LCG DT DT DT DT DG LCG DG LCG MODRES 2WCN LCG A 2 DG MODRES 2WCN LCG A 4 DG MODRES 2WCN LCG A 10 DG MODRES 2WCN LCG A 12 DG MODRES 2WCN LCG B 14 DG MODRES 2WCN LCG B 16 DG MODRES 2WCN LCG B 22 DG MODRES 2WCN LCG B 24 DG HET LCG A 2 35 HET LCG A 4 35 HET LCG A 10 35 HET LCG A 12 36 HET LCG B 14 35 HET LCG B 16 35 HET LCG B 22 35 HET LCG B 24 36 HETNAM LCG [(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5- HETNAM 2 LCG DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCG PHOSPHATE FORMUL 1 LCG 8(C11 H14 N5 O8 P) LINK O3' DG A 1 P LCG A 2 1555 1555 1.62 LINK O3' LCG A 2 P DG A 3 1555 1555 1.62 LINK O3' DG A 3 P LCG A 4 1555 1555 1.62 LINK O3' LCG A 4 P DT A 5 1555 1555 1.62 LINK O3' DG A 9 P LCG A 10 1555 1555 1.63 LINK O3' LCG A 10 P DG A 11 1555 1555 1.63 LINK O3' DG A 11 P LCG A 12 1555 1555 1.63 LINK O3' DG B 13 P LCG B 14 1555 1555 1.62 LINK O3' LCG B 14 P DG B 15 1555 1555 1.62 LINK O3' DG B 15 P LCG B 16 1555 1555 1.62 LINK O3' LCG B 16 P DT B 17 1555 1555 1.62 LINK O3' DG B 21 P LCG B 22 1555 1555 1.63 LINK O3' LCG B 22 P DG B 23 1555 1555 1.63 LINK O3' DG B 23 P LCG B 24 1555 1555 1.62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 2 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