PDB Short entry for 2CHK HEADER NUCLEIC ACID 15-MAR-06 2CHK TITLE NMR STRUCTURE OF TLLLLT QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*T LCG LCG LCG LCGP*TP)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 OTHER_DETAILS: TELOMERIC SEQUENCE FROM O. NOVA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS QUADRUPLEX, LNA, LOCKED NUCLEIC ACID, NUCLEIC ACID EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.T.NIELSEN,M.PETERSEN REVDAT 2 24-FEB-09 2CHK 1 VERSN REVDAT 1 19-APR-06 2CHK 0 JRNL AUTH J.T.NIELSEN,K.ARAR,M.PETERSEN JRNL TITL NMR SOLUTION STRUCTURES OF LNA (LOCKED NUCLEIC JRNL TITL 2 ACID) MODIFIED QUADRUPLEXES JRNL REF NUCLEIC ACIDS RES. V. 34 2006 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16614450 JRNL DOI 10.1093/NAR/GKL144 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 2CHK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-06. REMARK 100 THE PDBE ID CODE IS EBI-28159. 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 : 100MM REMARK 210 PRESSURE : 1.0 REMARK 210 SAMPLE CONTENTS : D20,10% D20/90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY;COSY;TOCSY;HSQC 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 : 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 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 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT A 6 O3' - P - O5' ANGL. DEV. = -16.2 DEGREES REMARK 500 1 DT A 6 O3' - P - OP1 ANGL. DEV. = -13.9 DEGREES REMARK 500 1 DT A 6 O3' - P - OP2 ANGL. DEV. = -13.9 DEGREES REMARK 500 1 DT A 6 C3' - O3' - P ANGL. DEV. = -38.0 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 12 C5' - C4' - C3' ANGL. DEV. = -8.3 DEGREES REMARK 500 1 DT B 12 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 12 O4' - C4' - C3' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DT B 12 O3' - P - O5' ANGL. DEV. = -48.2 DEGREES REMARK 500 1 DT B 12 C3' - O3' - P ANGL. DEV. = -31.5 DEGREES REMARK 500 1 DT C 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT C 18 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT C 18 O3' - P - O5' ANGL. DEV. = 11.7 DEGREES REMARK 500 1 DT C 18 O3' - P - OP1 ANGL. DEV. = 27.1 DEGREES REMARK 500 1 DT C 18 O3' - P - OP2 ANGL. DEV. = 27.1 DEGREES REMARK 500 1 DT C 18 C3' - O3' - P ANGL. DEV. = -33.1 DEGREES REMARK 500 1 DT D 19 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT D 24 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT D 24 O4' - C1' - C2' ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT D 24 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT D 24 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT D 24 O3' - P - O5' ANGL. DEV. = -39.4 DEGREES REMARK 500 1 DT D 24 O3' - P - OP1 ANGL. DEV. = 56.8 DEGREES REMARK 500 1 DT D 24 O3' - P - OP2 ANGL. DEV. = 56.8 DEGREES REMARK 500 1 DT D 24 C3' - O3' - P ANGL. DEV. = -30.8 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT A 6 O3' - P - OP1 ANGL. DEV. = 30.5 DEGREES REMARK 500 2 DT A 6 O3' - P - OP2 ANGL. DEV. = 30.5 DEGREES REMARK 500 2 DT A 6 C3' - O3' - P ANGL. DEV. = -32.1 DEGREES REMARK 500 2 DT B 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DT B 12 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 2 DT B 12 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT B 12 O4' - C4' - C3' ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DT B 12 O3' - P - O5' ANGL. DEV. = -48.7 DEGREES REMARK 500 2 DT B 12 C3' - O3' - P ANGL. DEV. = -31.4 DEGREES REMARK 500 2 DT C 13 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DT C 18 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT C 18 O3' - P - OP1 ANGL. DEV. = 33.6 DEGREES REMARK 500 2 DT C 18 O3' - P - OP2 ANGL. DEV. = 33.6 DEGREES REMARK 500 2 DT C 18 C3' - O3' - P ANGL. DEV. = -27.2 DEGREES REMARK 500 2 DT D 19 O4' - C1' - C2' ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DT D 19 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT D 24 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 620 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 DT A 6 0.10 SIDE CHAIN REMARK 500 1 DT B 7 0.07 SIDE CHAIN REMARK 500 1 DT C 18 0.11 SIDE CHAIN REMARK 500 2 DT A 6 0.12 SIDE CHAIN REMARK 500 2 DT B 7 0.06 SIDE CHAIN REMARK 500 2 DT C 13 0.06 SIDE CHAIN REMARK 500 2 DT C 18 0.10 SIDE CHAIN REMARK 500 3 DT B 12 0.13 SIDE CHAIN REMARK 500 4 DT A 6 0.11 SIDE CHAIN REMARK 500 4 DT C 18 0.12 SIDE CHAIN REMARK 500 5 DT A 6 0.10 SIDE CHAIN REMARK 500 5 DT C 18 0.14 SIDE CHAIN REMARK 500 6 DT B 12 0.09 SIDE CHAIN REMARK 500 6 DT D 19 0.06 SIDE CHAIN REMARK 500 6 DT D 24 0.12 SIDE CHAIN REMARK 500 7 DT B 12 0.11 SIDE CHAIN REMARK 500 8 DT A 1 0.07 SIDE CHAIN REMARK 500 8 DT B 7 0.07 SIDE CHAIN REMARK 500 8 DT B 12 0.12 SIDE CHAIN REMARK 500 8 DT D 19 0.07 SIDE CHAIN REMARK 500 8 DT D 24 0.12 SIDE CHAIN REMARK 500 9 DT B 12 0.12 SIDE CHAIN REMARK 500 9 DT D 24 0.12 SIDE CHAIN REMARK 500 10 DT B 12 0.10 SIDE CHAIN REMARK 500 10 DT D 24 0.10 SIDE CHAIN REMARK 500 11 DT A 6 0.06 SIDE CHAIN REMARK 500 11 DT C 18 0.08 SIDE CHAIN REMARK 500 12 DT A 1 0.07 SIDE CHAIN REMARK 500 12 DT B 12 0.11 SIDE CHAIN REMARK 500 12 DT C 13 0.07 SIDE CHAIN REMARK 500 12 DT D 24 0.07 SIDE CHAIN REMARK 500 13 DT A 6 0.12 SIDE CHAIN REMARK 500 13 DT C 18 0.11 SIDE CHAIN REMARK 500 14 DT A 6 0.07 SIDE CHAIN REMARK 500 14 DT C 13 0.07 SIDE CHAIN REMARK 500 14 DT C 18 0.10 SIDE CHAIN REMARK 500 15 DT C 18 0.10 SIDE CHAIN REMARK 500 16 DT A 6 0.10 SIDE CHAIN REMARK 500 16 DT C 18 0.06 SIDE CHAIN REMARK 500 16 DT D 19 0.06 SIDE CHAIN REMARK 500 17 DT A 6 0.11 SIDE CHAIN REMARK 500 17 DT B 7 0.08 SIDE CHAIN REMARK 500 17 DT C 18 0.13 SIDE CHAIN REMARK 500 18 DT A 1 0.06 SIDE CHAIN REMARK 500 18 DT D 19 0.07 SIDE CHAIN REMARK 500 18 DT D 24 0.12 SIDE CHAIN REMARK 500 19 DT B 7 0.06 SIDE CHAIN REMARK 500 19 DT B 12 0.09 SIDE CHAIN REMARK 500 19 DT C 13 0.08 SIDE CHAIN REMARK 500 19 DT D 24 0.11 SIDE CHAIN REMARK 500 20 DT A 6 0.10 SIDE CHAIN REMARK 500 20 DT C 18 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CHJ RELATED DB: PDB REMARK 900 NMR STRUCTURE OF TGLGLT QUADRUPLEX DBREF 2CHK A 1 6 PDB 2CHK 2CHK 1 6 DBREF 2CHK B 7 12 PDB 2CHK 2CHK 7 12 DBREF 2CHK C 13 18 PDB 2CHK 2CHK 13 18 DBREF 2CHK D 19 24 PDB 2CHK 2CHK 19 24 SEQRES 1 A 6 DT LCG LCG LCG LCG DT SEQRES 1 B 6 DT LCG LCG LCG LCG DT SEQRES 1 C 6 DT LCG LCG LCG LCG DT SEQRES 1 D 6 DT LCG LCG LCG LCG DT MODRES 2CHK LCG A 2 G LNA-GUANOSINE MODRES 2CHK LCG A 3 G LNA-GUANOSINE MODRES 2CHK LCG A 4 G LNA-GUANOSINE MODRES 2CHK LCG A 5 G LNA-GUANOSINE MODRES 2CHK LCG B 8 G LNA-GUANOSINE MODRES 2CHK LCG B 9 G LNA-GUANOSINE MODRES 2CHK LCG B 10 G LNA-GUANOSINE MODRES 2CHK LCG B 11 G LNA-GUANOSINE MODRES 2CHK LCG C 14 G LNA-GUANOSINE MODRES 2CHK LCG C 15 G LNA-GUANOSINE MODRES 2CHK LCG C 16 G LNA-GUANOSINE MODRES 2CHK LCG C 17 G LNA-GUANOSINE MODRES 2CHK LCG D 20 G LNA-GUANOSINE MODRES 2CHK LCG D 21 G LNA-GUANOSINE MODRES 2CHK LCG D 22 G LNA-GUANOSINE MODRES 2CHK LCG D 23 G LNA-GUANOSINE HET LCG A 2 35 HET LCG A 3 35 HET LCG A 4 35 HET LCG A 5 35 HET LCG B 8 35 HET LCG B 9 35 HET LCG B 10 35 HET LCG B 11 35 HET LCG C 14 35 HET LCG C 15 35 HET LCG C 16 35 HET LCG C 17 35 HET LCG D 20 35 HET LCG D 21 35 HET LCG D 22 35 HET LCG D 23 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 1 LCG 16(C11 H14 N5 O8 P) LINK O3' DT A 1 P LCG A 2 1555 1555 1.62 LINK O3' LCG A 2 P LCG A 3 1555 1555 1.61 LINK O3' LCG A 3 P LCG A 4 1555 1555 1.62 LINK O3' LCG A 4 P LCG A 5 1555 1555 1.61 LINK O3' LCG A 5 P DT A 6 1555 1555 1.62 LINK O3' DT B 7 P LCG B 8 1555 1555 1.63 LINK O3' LCG B 8 P LCG B 9 1555 1555 1.62 LINK O3' LCG B 9 P LCG B 10 1555 1555 1.62 LINK O3' LCG B 10 P LCG B 11 1555 1555 1.62 LINK O3' LCG B 11 P DT B 12 1555 1555 1.62 LINK O3' DT C 13 P LCG C 14 1555 1555 1.62 LINK O3' LCG C 14 P LCG C 15 1555 1555 1.62 LINK O3' LCG C 15 P LCG C 16 1555 1555 1.62 LINK O3' LCG C 16 P LCG C 17 1555 1555 1.61 LINK O3' LCG C 17 P DT C 18 1555 1555 1.64 LINK O3' DT D 19 P LCG D 20 1555 1555 1.64 LINK O3' LCG D 20 P LCG D 21 1555 1555 1.61 LINK O3' LCG D 21 P LCG D 22 1555 1555 1.62 LINK O3' LCG D 22 P LCG D 23 1555 1555 1.61 LINK O3' LCG D 23 P DT D 24 1555 1555 1.64 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 4 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