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 OTHER_DETAILS: MODEL SYSTEM DERIVED FROM OXYTRICIA NOVA COMPND 7 TELOMERE SEQUNCE MODIFIED WITH LNA NUCLEOTIDES AT COMPND 8 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 1 24-NOV-09 2WCN 0 JRNL AUTH J.T.NIELSEN,K.ARAR,M.PETERSEN JRNL TITL SOLUTION STRUCTURE OF A LOCKED NUCLEIC ACID JRNL TITL 2 MODIFIED QUADRUPLEX: INTRODUCING THE V4 FOLDING JRNL TITL 3 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 : X-PLOR NIH 2.14 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2WCN COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAR-09. REMARK 100 THE PDBE ID CODE IS EBI-39034. 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 MM 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 REMARK 210 SPECTROMETER MODEL : UNITYINOVA 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 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 N9 DG A 1 C8 -0.046 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 DT A 6 P DT A 6 O5' 0.073 REMARK 500 1 DG A 11 C5' DG A 11 C4' 0.043 REMARK 500 1 DG B 13 N9 DG B 13 C8 -0.047 REMARK 500 1 DT B 18 C5 DT B 18 C7 0.057 REMARK 500 2 DG A 1 N9 DG A 1 C8 -0.049 REMARK 500 2 DT A 6 C3' DT A 6 C2' -0.057 REMARK 500 2 DT A 6 P DT A 6 O5' 0.062 REMARK 500 2 DG A 11 C5' DG A 11 C4' 0.044 REMARK 500 2 DG B 13 N9 DG B 13 C8 -0.047 REMARK 500 2 DT B 18 C2' DT B 18 C1' -0.065 REMARK 500 2 DT B 18 C3' DT B 18 C2' -0.052 REMARK 500 2 DT B 18 C5' DT B 18 C4' 0.043 REMARK 500 2 DT B 18 P DT B 18 O5' 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 N9 DG A 1 C8 -0.052 REMARK 500 3 DT A 5 C2' DT A 5 C1' -0.069 REMARK 500 3 DT A 5 N1 DT A 5 C6 -0.088 REMARK 500 3 DT A 6 C5 DT A 6 C7 0.041 REMARK 500 3 DG B 13 N9 DG B 13 C8 -0.050 REMARK 500 3 DT B 17 C2' DT B 17 C1' -0.078 REMARK 500 3 DT B 17 N1 DT B 17 C6 -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 C4' DT A 5 O4' -0.060 REMARK 500 4 DT A 6 C2' DT A 6 C1' -0.063 REMARK 500 4 DT A 6 C3' DT A 6 C2' -0.051 REMARK 500 4 DT A 6 P DT A 6 O5' 0.061 REMARK 500 4 DG A 9 C4' DG A 9 O4' -0.060 REMARK 500 4 DG B 13 C2' DG B 13 C1' -0.061 REMARK 500 4 DG B 13 N9 DG B 13 C8 -0.047 REMARK 500 4 DT B 18 C2' DT B 18 C1' -0.061 REMARK 500 4 DT B 18 C3' DT B 18 C2' -0.052 REMARK 500 4 DT B 20 C4' DT B 20 O4' -0.061 REMARK 500 5 DG A 1 N9 DG A 1 C8 -0.050 REMARK 500 5 DT A 5 C2' DT A 5 C1' -0.101 REMARK 500 5 DT A 5 N1 DT A 5 C6 -0.086 REMARK 500 5 DT A 6 C5 DT A 6 C7 0.044 REMARK 500 5 DG B 13 N9 DG B 13 C8 -0.044 REMARK 500 5 DT B 17 C2' DT B 17 C1' -0.142 REMARK 500 5 DT B 17 C3' DT B 17 C2' -0.052 REMARK 500 5 DT B 17 N1 DT B 17 C6 -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 6 DG A 1 N9 DG A 1 C8 -0.050 REMARK 500 REMARK 500 THIS ENTRY HAS 159 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 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DG A 3 N3 - C4 - C5 ANGL. DEV. = -3.3 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 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 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 6 C4 - C5 - C7 ANGL. DEV. = -3.6 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 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 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG B 13 O4' - C1' - N9 ANGL. DEV. = 6.7 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 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 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 18 O4' - C1' - N1 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 19 O5' - C5' - C4' ANGL. DEV. = 18.4 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 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 1 C4 - N9 - C1' ANGL. DEV. = 9.8 DEGREES REMARK 500 2 DG A 1 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 3 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DT A 5 C3' - C2' - C1' ANGL. DEV. = 13.0 DEGREES REMARK 500 2 DT A 5 C4' - C3' - C2' ANGL. DEV. = -9.2 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 O4' - C4' - C3' ANGL. DEV. = 11.6 DEGREES REMARK 500 2 DT A 6 C3' - C2' - C1' ANGL. DEV. = 8.0 DEGREES REMARK 500 2 DT A 6 C4' - C3' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 6 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1004 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 0.06 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 0.06 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 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 6 DT A 5 -24.2 D D OUTSIDE RANGE REMARK 500 11 DT A 5 -24.2 D D OUTSIDE RANGE REMARK 500 12 DT A 6 -45.1 D D OUTSIDE RANGE REMARK 500 12 DT B 18 -45.2 D D OUTSIDE RANGE REMARK 500 19 DT A 5 -24.2 D D OUTSIDE RANGE 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 MODIFIED GUANOSINE NUCLEOTIDE MODRES 2WCN LCG A 4 DG MODIFIED GUANOSINE NUCLEOTIDE MODRES 2WCN LCG A 10 DG MODIFIED GUANOSINE NUCLEOTIDE MODRES 2WCN LCG A 12 DG MODIFIED GUANOSINE NUCLEOTIDE MODRES 2WCN LCG B 14 DG MODIFIED GUANOSINE NUCLEOTIDE MODRES 2WCN LCG B 16 DG MODIFIED GUANOSINE NUCLEOTIDE MODRES 2WCN LCG B 22 DG MODIFIED GUANOSINE NUCLEOTIDE MODRES 2WCN LCG B 24 DG MODIFIED GUANOSINE NUCLEOTIDE 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 35 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 HETNAM 3 LCG DIHYDROGEN PHOSPHATE FORMUL 3 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 1.62 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 239 0 8 0 0 0 0 6 0 0 0 2 END