HEADER RNA 19-JAN-06 2DD1 TITLE THREE CONSECUTIVE SHEARED GA PAIRS IN 5'GGUGGAGGCU/3'PCCAAAGCCG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*UP*GP*GP*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*AP*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 THREE CONSECUTIVE SHEARED GA PAIRS, THERMODYNAMICS OF MOLECULAR KEYWDS 2 RECOGNITION, K-TURN MOTIF, A-MINOR MOTIF, SECONDARY STRUCTURE OF KEYWDS 3 RNA, RNA EXPDTA SOLUTION NMR NUMMDL 24 AUTHOR G.CHEN,S.D.KENNEDY,T.R.KRUGH,D.H.TURNER REVDAT 4 09-MAR-22 2DD1 1 REMARK LINK REVDAT 3 21-JUL-09 2DD1 1 HET HETATM HETNAM MODRES REVDAT 3 2 1 FORMUL LINK SEQRES COMPND REVDAT 2 24-FEB-09 2DD1 1 VERSN REVDAT 1 13-JUN-06 2DD1 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 STABILITY FOR JRNL TITL 2 A SINGLE SHEARED PURINE-PURINE PAIR FLANKED BY SHEARED GA JRNL TITL 3 PAIRS IN RNA JRNL REF BIOCHEMISTRY V. 45 6889 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16734425 JRNL DOI 10.1021/BI0524464 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX, DISCOVER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DD1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000025270. 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, PH REMARK 210 5.4, PD 6.8 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL 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 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 : 24 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 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 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 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 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. = 4.6 DEGREES REMARK 500 2 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 3 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 4 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 5 G A 7 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 5 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 5 C B 19 O4' - C1' - N1 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. = 4.8 DEGREES REMARK 500 6 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.0 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. = 5.0 DEGREES REMARK 500 7 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 7 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 8 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 8 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 8 U A 10 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 8 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 9 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 9 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 C B 19 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 10 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 10 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 10 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 11 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 11 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 11 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 11 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 118 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 G A 5 0.06 SIDE CHAIN REMARK 500 2 G A 8 0.06 SIDE CHAIN REMARK 500 2 A B 17 0.07 SIDE CHAIN REMARK 500 3 G A 4 0.05 SIDE CHAIN REMARK 500 3 G B 14 0.06 SIDE CHAIN REMARK 500 4 G B 11 0.06 SIDE CHAIN REMARK 500 4 A B 17 0.06 SIDE CHAIN REMARK 500 6 G A 4 0.06 SIDE CHAIN REMARK 500 7 A B 16 0.07 SIDE CHAIN REMARK 500 7 A B 17 0.06 SIDE CHAIN REMARK 500 8 G B 11 0.07 SIDE CHAIN REMARK 500 8 A B 17 0.05 SIDE CHAIN REMARK 500 9 G B 14 0.06 SIDE CHAIN REMARK 500 10 G A 5 0.07 SIDE CHAIN REMARK 500 10 G B 11 0.06 SIDE CHAIN REMARK 500 10 A B 17 0.07 SIDE CHAIN REMARK 500 11 A B 16 0.07 SIDE CHAIN REMARK 500 11 A B 17 0.07 SIDE CHAIN REMARK 500 12 G A 5 0.06 SIDE CHAIN REMARK 500 13 G B 14 0.06 SIDE CHAIN REMARK 500 14 G A 5 0.09 SIDE CHAIN REMARK 500 14 G B 11 0.06 SIDE CHAIN REMARK 500 14 A B 17 0.06 SIDE CHAIN REMARK 500 15 A B 16 0.08 SIDE CHAIN REMARK 500 15 A B 17 0.10 SIDE CHAIN REMARK 500 16 G B 14 0.06 SIDE CHAIN REMARK 500 17 G A 5 0.05 SIDE CHAIN REMARK 500 17 A B 17 0.06 SIDE CHAIN REMARK 500 18 A B 16 0.07 SIDE CHAIN REMARK 500 18 A B 17 0.10 SIDE CHAIN REMARK 500 19 G A 5 0.07 SIDE CHAIN REMARK 500 20 G A 4 0.07 SIDE CHAIN REMARK 500 20 G A 5 0.06 SIDE CHAIN REMARK 500 21 G B 14 0.06 SIDE CHAIN REMARK 500 21 A B 16 0.06 SIDE CHAIN REMARK 500 21 A B 17 0.06 SIDE CHAIN REMARK 500 22 G B 11 0.07 SIDE CHAIN REMARK 500 22 A B 16 0.05 SIDE CHAIN REMARK 500 22 A B 17 0.06 SIDE CHAIN REMARK 500 22 C B 19 0.07 SIDE CHAIN REMARK 500 23 G A 5 0.06 SIDE CHAIN REMARK 500 24 G A 5 0.06 SIDE CHAIN REMARK 500 24 A B 16 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DD2 RELATED DB: PDB REMARK 900 5'GGUGGAGGCU/3'PCCAAAGCCG REMARK 900 RELATED ID: 2DD3 RELATED DB: PDB REMARK 900 A SINGLE SHEARED PURINE-PURINE PAIR FLANKED BY SHEARED GA PAIRS, 5' REMARK 900 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 2DD1 A 1 10 PDB 2DD1 2DD1 1 10 DBREF 2DD1 B 11 20 PDB 2DD1 2DD1 11 20 SEQRES 1 A 10 G G U G G A G G C U SEQRES 1 B 10 G C C G A A A C C P5P MODRES 2DD1 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 MODEL 1