10 20 30 40 50 60 70 80 2DD2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 19-JAN-06 2DD2
TITLE AN ALTERNATING SHEARED AA PAIR IN 5'GGUGAAGGCU/3'PCCGAAGCCG: TITLE 2 I. THE MAJOR CONFORMATION WITH A6/A15/A16 STACK
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P))-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS ALTERNATING, CONFORMATION EXCHANGE, DYNAMICS, SHEARED AA KEYWDS 2 PAIR, SHEARED GA PAIR, THERMODYNAMICS, RNA SECONDARY KEYWDS 3 STRUCTURE, A-MINOR MOTIF, KINK-TURN
EXPDTA SOLUTION NMR
NUMMDL 27
AUTHOR G.CHEN,S.D.KENNEDY,T.R.KRUGH,D.H.TURNER
REVDAT 3 21-JUL-09 2DD2 1 HET HETATM HETNAM MODRES REVDAT 3 2 1 FORMUL LINK SEQRES COMPND REVDAT 2 24-FEB-09 2DD2 1 VERSN REVDAT 1 13-JUN-06 2DD2 0
JRNL AUTH G.CHEN,S.D.KENNEDY,J.QIAO,T.R.KRUGH,D.H.TURNER JRNL TITL AN ALTERNATING SHEARED AA PAIR AND ELEMENTS OF JRNL TITL 2 STABILITY FOR A SINGLE SHEARED PURINE-PURINE PAIR JRNL TITL 3 FLANKED BY SHEARED GA PAIRS IN RNA JRNL REF BIOCHEMISTRY V. 45 6889 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16734425 JRNL DOI 10.1021/BI0524464
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2DD2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-06. REMARK 100 THE RCSB ID CODE IS RCSB025271.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 80MM NACL, 10MM SODIUM REMARK 210 PHOSPHATE, 0.5MM NA2EDTA, 2MM REMARK 210 TOTAL DUPLEX CONCENTRATIONS, REMARK 210 PH 5.1, PD 7.3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, VNMR REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 27 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY, STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS 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 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 G A 7 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G B 14 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 2 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 U A 3 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 G A 7 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 4 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 5 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 6 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 6 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 7 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 7 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 8 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 8 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 8 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 8 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 9 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 9 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 9 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 9 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 9 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 10 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 139 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 2 A A 5 0.06 SIDE_CHAIN REMARK 500 2 A B 15 0.08 SIDE_CHAIN REMARK 500 2 A B 16 0.06 SIDE_CHAIN REMARK 500 3 A A 5 0.06 SIDE_CHAIN REMARK 500 4 A A 5 0.06 SIDE_CHAIN REMARK 500 5 A A 5 0.06 SIDE_CHAIN REMARK 500 5 G B 11 0.06 SIDE_CHAIN REMARK 500 6 A B 16 0.06 SIDE_CHAIN REMARK 500 7 A A 5 0.07 SIDE_CHAIN REMARK 500 7 A B 15 0.06 SIDE_CHAIN REMARK 500 7 A B 16 0.05 SIDE_CHAIN REMARK 500 8 A B 15 0.06 SIDE_CHAIN REMARK 500 8 A B 16 0.07 SIDE_CHAIN REMARK 500 8 C B 18 0.07 SIDE_CHAIN REMARK 500 9 G A 4 0.05 SIDE_CHAIN REMARK 500 9 A A 5 0.06 SIDE_CHAIN REMARK 500 10 A A 5 0.07 SIDE_CHAIN REMARK 500 11 G B 11 0.06 SIDE_CHAIN REMARK 500 12 A A 5 0.06 SIDE_CHAIN REMARK 500 12 G B 11 0.07 SIDE_CHAIN REMARK 500 12 A B 15 0.07 SIDE_CHAIN REMARK 500 13 A B 15 0.07 SIDE_CHAIN REMARK 500 15 A B 15 0.06 SIDE_CHAIN REMARK 500 15 A B 16 0.06 SIDE_CHAIN REMARK 500 16 G B 14 0.07 SIDE_CHAIN REMARK 500 16 A B 15 0.06 SIDE_CHAIN REMARK 500 16 A B 16 0.06 SIDE_CHAIN REMARK 500 17 A B 15 0.06 SIDE_CHAIN REMARK 500 18 A A 5 0.06 SIDE_CHAIN REMARK 500 19 A A 5 0.08 SIDE_CHAIN REMARK 500 19 A B 15 0.07 SIDE_CHAIN REMARK 500 19 A B 16 0.05 SIDE_CHAIN REMARK 500 20 A B 15 0.06 SIDE_CHAIN REMARK 500 20 A B 16 0.06 SIDE_CHAIN REMARK 500 21 A A 5 0.06 SIDE_CHAIN REMARK 500 22 A B 15 0.06 SIDE_CHAIN REMARK 500 22 A B 16 0.07 SIDE_CHAIN REMARK 500 23 A A 5 0.06 SIDE_CHAIN REMARK 500 23 G B 11 0.06 SIDE_CHAIN REMARK 500 23 A B 16 0.06 SIDE_CHAIN REMARK 500 24 A A 5 0.06 SIDE_CHAIN REMARK 500 24 A B 15 0.06 SIDE_CHAIN REMARK 500 24 A B 16 0.07 SIDE_CHAIN REMARK 500 24 C B 19 0.07 SIDE_CHAIN REMARK 500 26 G B 11 0.06 SIDE_CHAIN REMARK 500 26 A B 15 0.06 SIDE_CHAIN REMARK 500 27 A A 5 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DD1 RELATED DB: PDB REMARK 900 3 SHEARED GA PAIRS CLOSED BY UA AND CG WC PAIRS, 5' REMARK 900 GGUGGAGGCU/3'PCCAAAGCCG REMARK 900 RELATED ID: 2DD3 RELATED DB: PDB REMARK 900 A SINGLE SHEARED PURINE-PURINE PAIR FLANKED BY SHEARED GA REMARK 900 PAIRS, 5'GGUGAAGGCU/3'PCCGAAGCCG REMARK 900 RELATED ID: 1XV0 RELATED DB: PDB REMARK 900 3 SHEARED GA PAIRS CLOSED BY UG WOBBLE AND CG WC PAIRS, 5' REMARK 900 GGUGGAGGCU/3'PCCGAAGCCG
DBREF 2DD2 A 1 10 PDB 2DD2 2DD2 1 10 DBREF 2DD2 B 11 20 PDB 2DD2 2DD2 11 20
SEQRES 1 A 10 G G U G A A G G C U SEQRES 1 B 10 G C C G A A G C C P5P
MODRES 2DD2 P5P B 20 A PURINE RIBOSIDE-5'-MONOPHOSPHATE
HET P5P B 20 32
HETNAM P5P PURINE RIBOSIDE-5'-MONOPHOSPHATE
FORMUL 2 P5P C10 H13 N4 O7 P
LINK O3' C B 19 P P5P B 20 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