10 20 30 40 50 60 70 80 2RMQ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 12-NOV-07 2RMQ
TITLE SOLUTION STRUCTURE OF FULLY MODIFIED 4'-THIODNA WITH THE TITLE 2 SEQUENCE OF D(CGCGAATTCGCG)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(C4S)P*(S4G)P*(C4S)P*(S4G)P*(S4A) COMPND 3 P*(S4A)P*(T49)P*(T49)P*(C4S)P*(S4G)P*(C4S)P*(S4G))-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: 4'-THIO-DNA
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS 4'-THIODNA, A-FORM
EXPDTA SOLUTION NMR
AUTHOR A.MATSUGAMI,T.OHYAMA,M.INADA,M.KATAHIRA
REVDAT 2 24-FEB-09 2RMQ 1 VERSN REVDAT 1 15-APR-08 2RMQ 0
JRNL AUTH A.MATSUGAMI,T.OHYAMA,M.INADA,N.INOUE,N.MINAKAWA, JRNL AUTH 2 A.MATSUDA,M.KATAHIRA JRNL TITL UNEXPECTED A-FORM FORMATION OF 4'-THIODNA IN JRNL TITL 2 SOLUTION, REVEALED BY NMR, AND THE IMPLICATIONS AS JRNL TITL 3 TO THE MECHANISM OF NUCLEASE RESISTANCE JRNL REF NUCLEIC ACIDS RES. V. 36 1805 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18252770 JRNL DOI 10.1093/NAR/GKN011
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNSSOLVE 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2RMQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-NOV-07. REMARK 100 THE RCSB ID CODE IS RCSB150041.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 20; 20 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.42MM 4'-THIO DNA; 10MM REMARK 210 SODIUM PHOSPHATE; 10MM SODIUM REMARK 210 CHLORIDE; 0.01MM DSS; 95% H2O, REMARK 210 5% D2O; 0.42MM 4'-THIO DNA; REMARK 210 10MM SODIUM PHOSPHATE; 10MM REMARK 210 SODIUM CHLORIDE; 0.01MM DSS; REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY, 2D 1H-1H TOCSY, REMARK 210 2D 1H-1H NOESY, 2D 1H-13C REMARK 210 HSQC, 2D 1H-13C JR-HMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, TOPSPIN 1.0, REMARK 210 NMRPIPE 2.4, NMRDRAW 2.4, REMARK 210 SPARKY 3.111, CNSSOLVE 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL
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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 RES CSSEQI ATOMS REMARK 470 C4S A 1 O1P O2P REMARK 470 C4S B 13 O1P O2P
DBREF 2RMQ A 1 12 PDB 2RMQ 2RMQ 1 12 DBREF 2RMQ B 13 24 PDB 2RMQ 2RMQ 13 24
SEQRES 1 A 12 C4S S4G C4S S4G S4A S4A T49 T49 C4S S4G C4S S4G SEQRES 1 B 12 C4S S4G C4S S4G S4A S4A T49 T49 C4S S4G C4S S4G
MODRES 2RMQ C4S A 1 DC MODRES 2RMQ S4G A 2 DG MODRES 2RMQ C4S A 3 DC MODRES 2RMQ S4G A 4 DG MODRES 2RMQ S4A A 5 DA MODRES 2RMQ S4A A 6 DA MODRES 2RMQ T49 A 7 DT S4'-2'DEOXYTHYMIDINE 5'-MONOPHOSPHATE MODRES 2RMQ T49 A 8 DT S4'-2'DEOXYTHYMIDINE 5'-MONOPHOSPHATE MODRES 2RMQ C4S A 9 DC MODRES 2RMQ S4G A 10 DG MODRES 2RMQ C4S A 11 DC MODRES 2RMQ S4G A 12 DG MODRES 2RMQ C4S B 13 DC MODRES 2RMQ S4G B 14 DG MODRES 2RMQ C4S B 15 DC MODRES 2RMQ S4G B 16 DG MODRES 2RMQ S4A B 17 DA MODRES 2RMQ S4A B 18 DA MODRES 2RMQ T49 B 19 DT S4'-2'DEOXYTHYMIDINE 5'-MONOPHOSPHATE MODRES 2RMQ T49 B 20 DT S4'-2'DEOXYTHYMIDINE 5'-MONOPHOSPHATE MODRES 2RMQ C4S B 21 DC MODRES 2RMQ S4G B 22 DG MODRES 2RMQ C4S B 23 DC MODRES 2RMQ S4G B 24 DG
HET C4S A 1 28 HET S4G A 2 33 HET C4S A 3 30 HET S4G A 4 33 HET S4A A 5 32 HET S4A A 6 32 HET T49 A 7 32 HET T49 A 8 32 HET C4S A 9 30 HET S4G A 10 33 HET C4S A 11 30 HET S4G A 12 34 HET C4S B 13 28 HET S4G B 14 33 HET C4S B 15 30 HET S4G B 16 33 HET S4A B 17 32 HET S4A B 18 32 HET T49 B 19 32 HET T49 B 20 32 HET C4S B 21 30 HET S4G B 22 33 HET C4S B 23 30 HET S4G B 24 34
HETNAM C4S 2'-DEOXY-4'-THIOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM S4G 2'-DEOXY-4'-THIOGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM S4A 2'-DEOXY-4'-THIOADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM T49 S4'-2'DEOXYTHYMIDINE 5'-MONOPHOSPHATE
FORMUL 1 C4S 8(C9 H14 N3 O6 P S) FORMUL 1 S4G 8(C10 H14 N5 O6 P S) FORMUL 1 S4A 4(C10 H14 N5 O5 P S) FORMUL 1 T49 4(C10 H15 N2 O7 P S)
LINK O3' C4S A 1 P S4G A 2 1555 1555 1.61 LINK O3' S4G A 2 P C4S A 3 1555 1555 1.61 LINK O3' C4S A 3 P S4G A 4 1555 1555 1.61 LINK O3' S4G A 4 P S4A A 5 1555 1555 1.61 LINK O3' S4A A 5 P S4A A 6 1555 1555 1.61 LINK O3' S4A A 6 P T49 A 7 1555 1555 1.61 LINK O3' T49 A 7 P T49 A 8 1555 1555 1.61 LINK O3' T49 A 8 P C4S A 9 1555 1555 1.61 LINK O3' C4S A 9 P S4G A 10 1555 1555 1.61 LINK O3' S4G A 10 P C4S A 11 1555 1555 1.61 LINK O3' C4S A 11 P S4G A 12 1555 1555 1.61 LINK O3' C4S B 13 P S4G B 14 1555 1555 1.61 LINK O3' S4G B 14 P C4S B 15 1555 1555 1.61 LINK O3' C4S B 15 P S4G B 16 1555 1555 1.61 LINK O3' S4G B 16 P S4A B 17 1555 1555 1.61 LINK O3' S4A B 17 P S4A B 18 1555 1555 1.61 LINK O3' S4A B 18 P T49 B 19 1555 1555 1.61 LINK O3' T49 B 19 P T49 B 20 1555 1555 1.61 LINK O3' T49 B 20 P C4S B 21 1555 1555 1.61 LINK O3' C4S B 21 P S4G B 22 1555 1555 1.61 LINK O3' S4G B 22 P C4S B 23 1555 1555 1.61 LINK O3' C4S B 23 P S4G B 24 1555 1555 1.61
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