10 20 30 40 50 60 70 80 2O81 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 11-DEC-06 2O81
TITLE THE STRUCTURE OF TANDEM GA RNA PAIRS WHEN FLANKING PAIRS TITLE 2 ARE ISOG-ISOC PAIRS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*CP*(IG)P*GP*AP*(IC)P*GP*CP*A)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS RNA, THERMODYNAMICS, SECONDARY STRUCTURE PREDICTION, KEYWDS 2 SHEARED GA PAIR, ISOGUANOSINE, ISOCYTIDINE
EXPDTA SOLUTION NMR
NUMMDL 18
AUTHOR G.CHEN,D.H.TURNER
REVDAT 2 24-FEB-09 2O81 1 VERSN REVDAT 1 10-JUL-07 2O81 0
JRNL AUTH G.CHEN,R.KIERZEK,I.YILDIRIM,T.R.KRUGH,D.H.TURNER, JRNL AUTH 2 S.D.KENNEDY JRNL TITL STACKING EFFECTS ON LOCAL STRUCTURE IN RNA: JRNL TITL 2 CHANGES IN THE STRUCTURE OF TANDEM GA PAIRS WHEN JRNL TITL 3 FLANKING GC PAIRS ARE REPLACED BY ISOG-ISOC PAIRS JRNL REF J.PHYS.CHEM.B V. 111 6718 2007 JRNL REFN ISSN 1089-5647 JRNL PMID 17411085 JRNL DOI 10.1021/JP068732M
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER I2000 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS, INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2O81 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-07. REMARK 100 THE RCSB ID CODE IS RCSB040803.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 80 MM NACL, 10 MM SODIUM REMARK 210 PHOSPHATE, 0.5 MM NA2EDTA, PH REMARK 210 7.1, 0.7MM RNA DUPLEX REMARK 210 CONCENTRATION, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1C, NMRPIPE 2.3, REMARK 210 SPARKY 3.11, DISCOVER I2000 REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 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 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 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 8 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 9 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 10 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 C A 8 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 10 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 11 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 12 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 12 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 13 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 13 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 13 C B 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 14 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 14 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 15 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 16 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 16 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 16 C B 8 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 17 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 17 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 17 C B 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 18 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 18 C B 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES 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 G A 1 0.07 SIDE_CHAIN REMARK 500 1 G A 7 0.06 SIDE_CHAIN REMARK 500 1 G B 1 0.07 SIDE_CHAIN REMARK 500 1 G B 7 0.06 SIDE_CHAIN REMARK 500 2 G A 1 0.07 SIDE_CHAIN REMARK 500 2 G A 7 0.06 SIDE_CHAIN REMARK 500 2 G B 1 0.07 SIDE_CHAIN REMARK 500 2 G B 7 0.06 SIDE_CHAIN REMARK 500 3 G A 1 0.07 SIDE_CHAIN REMARK 500 3 G A 7 0.06 SIDE_CHAIN REMARK 500 3 G B 1 0.07 SIDE_CHAIN REMARK 500 3 G B 7 0.06 SIDE_CHAIN REMARK 500 4 G A 1 0.07 SIDE_CHAIN REMARK 500 4 G A 7 0.06 SIDE_CHAIN REMARK 500 4 G B 1 0.07 SIDE_CHAIN REMARK 500 4 G B 7 0.06 SIDE_CHAIN REMARK 500 5 G A 1 0.07 SIDE_CHAIN REMARK 500 5 G A 7 0.06 SIDE_CHAIN REMARK 500 5 G B 1 0.07 SIDE_CHAIN REMARK 500 5 G B 7 0.06 SIDE_CHAIN REMARK 500 6 G A 1 0.07 SIDE_CHAIN REMARK 500 6 G A 7 0.06 SIDE_CHAIN REMARK 500 6 G B 1 0.07 SIDE_CHAIN REMARK 500 6 G B 7 0.06 SIDE_CHAIN REMARK 500 7 G A 1 0.07 SIDE_CHAIN REMARK 500 7 G B 1 0.07 SIDE_CHAIN REMARK 500 7 G B 7 0.06 SIDE_CHAIN REMARK 500 8 G A 1 0.07 SIDE_CHAIN REMARK 500 8 G A 7 0.06 SIDE_CHAIN REMARK 500 8 G B 1 0.07 SIDE_CHAIN REMARK 500 8 G B 7 0.06 SIDE_CHAIN REMARK 500 9 G A 1 0.07 SIDE_CHAIN REMARK 500 9 G A 7 0.06 SIDE_CHAIN REMARK 500 9 G B 1 0.07 SIDE_CHAIN REMARK 500 9 G B 7 0.06 SIDE_CHAIN REMARK 500 10 G A 1 0.07 SIDE_CHAIN REMARK 500 10 G B 1 0.06 SIDE_CHAIN REMARK 500 10 G B 7 0.06 SIDE_CHAIN REMARK 500 11 G A 1 0.07 SIDE_CHAIN REMARK 500 11 G A 7 0.07 SIDE_CHAIN REMARK 500 11 G B 1 0.07 SIDE_CHAIN REMARK 500 11 G B 7 0.06 SIDE_CHAIN REMARK 500 12 G A 1 0.07 SIDE_CHAIN REMARK 500 12 G A 7 0.06 SIDE_CHAIN REMARK 500 12 G B 1 0.07 SIDE_CHAIN REMARK 500 12 G B 7 0.06 SIDE_CHAIN REMARK 500 13 G A 1 0.07 SIDE_CHAIN REMARK 500 13 G A 7 0.06 SIDE_CHAIN REMARK 500 13 G B 1 0.07 SIDE_CHAIN REMARK 500 13 G B 7 0.06 SIDE_CHAIN REMARK 500 14 G A 1 0.07 SIDE_CHAIN REMARK 500 14 G A 7 0.06 SIDE_CHAIN REMARK 500 14 G B 1 0.07 SIDE_CHAIN REMARK 500 14 G B 7 0.06 SIDE_CHAIN REMARK 500 15 G A 1 0.07 SIDE_CHAIN REMARK 500 15 G A 7 0.06 SIDE_CHAIN REMARK 500 15 G B 1 0.07 SIDE_CHAIN REMARK 500 15 G B 7 0.06 SIDE_CHAIN REMARK 500 16 G A 1 0.07 SIDE_CHAIN REMARK 500 16 G A 7 0.06 SIDE_CHAIN REMARK 500 16 G B 1 0.07 SIDE_CHAIN REMARK 500 17 G A 1 0.07 SIDE_CHAIN REMARK 500 17 G A 7 0.06 SIDE_CHAIN REMARK 500 17 G B 1 0.07 SIDE_CHAIN REMARK 500 17 G B 7 0.06 SIDE_CHAIN REMARK 500 18 G A 1 0.07 SIDE_CHAIN REMARK 500 18 G A 7 0.07 SIDE_CHAIN REMARK 500 18 G B 1 0.07 SIDE_CHAIN REMARK 500 18 G B 7 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O83 RELATED DB: PDB REMARK 900 GG(IC)GA(IG)CCA
DBREF 2O81 A 1 9 PDB 2O81 2O81 1 9 DBREF 2O81 B 1 9 PDB 2O81 2O81 1 9
SEQRES 1 A 9 G C IG G A IC G C A SEQRES 1 B 9 G C IG G A IC G C A
MODRES 2O81 IG A 3 G ISOGUANOSINE-5'-MONOPHOSPHATE MODRES 2O81 IC A 6 C ISOCYTIDINE-5'-MONOPHOSPHATE MODRES 2O81 IG B 3 G ISOGUANOSINE-5'-MONOPHOSPHATE MODRES 2O81 IC B 6 C ISOCYTIDINE-5'-MONOPHOSPHATE
HET IG A 3 34 HET IC A 6 31 HET IG B 3 34 HET IC B 6 31
HETNAM IG ISOGUANOSINE-5'-MONOPHOSPHATE HETNAM IC ISOCYTIDINE-5'-MONOPHOSPHATE
FORMUL 1 IG 2(C10 H14 N5 O8 P) FORMUL 1 IC 2(C9 H14 N3 O8 P)
LINK O3' C A 2 P IG A 3 1555 1555 1.62 LINK O3' IG A 3 P G A 4 1555 1555 1.62 LINK O3' A A 5 P IC A 6 1555 1555 1.62 LINK O3' IC A 6 P G A 7 1555 1555 1.62 LINK O3' C B 2 P IG B 3 1555 1555 1.62 LINK O3' IG B 3 P G B 4 1555 1555 1.62 LINK O3' A B 5 P IC B 6 1555 1555 1.62 LINK O3' IC B 6 P G B 7 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