10 20 30 40 50 60 70 80 1XV0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 26-OCT-04 1XV0
TITLE SOLUTION NMR STRUCTURE OF RNA INTERNAL LOOP WITH THREE TITLE 2 CONSECUTIVE SHEARED GA PAIRS IN 5'GGUGGAGGCU/3'PCCGAAGCCG
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*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 THERMODYNAMICS AND STRUCTURE, BASE STACKING AND HYDROGEN KEYWDS 2 BONDING, 3-GA MOTIF, RNA
EXPDTA SOLUTION NMR
NUMMDL 33
AUTHOR G.CHEN,B.M.ZNOSKO,S.D.KENNEDY,T.R.KRUGH,D.H.TURNER
REVDAT 4 24-FEB-09 1XV0 1 VERSN REVDAT 3 15-MAR-05 1XV0 1 REVDAT REVDAT 2 07-MAR-05 1XV0 1 JRNL REVDAT 1 09-NOV-04 1XV0 0
JRNL AUTH G.CHEN,B.M.ZNOSKO,S.D.KENNEDY,T.R.KRUGH,D.H.TURNER JRNL TITL SOLUTION STRUCTURE OF AN RNA INTERNAL LOOP WITH JRNL TITL 2 THREE CONSECUTIVE SHEARED GA PAIRS JRNL REF BIOCHEMISTRY V. 44 2845 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15723528 JRNL DOI 10.1021/BI048079Y
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 1XV0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-04. REMARK 100 THE RCSB ID CODE IS RCSB030794.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 273 REMARK 210 PH : 5.9; 5.9 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 80 MM NACL, 10 MM SODIUM REMARK 210 PHOSPHATES, 0.5 MM EDTA, PH5.9 REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY, 2D NOESY, 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 : FELIX 2000, DISCOVER, AMBER REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 33 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 17 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 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. = 4.6 DEGREES REMARK 500 1 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 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. = 5.1 DEGREES REMARK 500 2 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 G A 2 O4' - C1' - N9 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. = 4.4 DEGREES REMARK 500 3 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 4 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 5 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.6 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. = 4.4 DEGREES REMARK 500 5 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 6 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 6 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 6 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.6 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. = 4.7 DEGREES REMARK 500 8 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 8 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.0 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. = 4.7 DEGREES REMARK 500 8 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.2 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. = 5.5 DEGREES REMARK 500 9 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 9 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.4 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. = 5.3 DEGREES REMARK 500 10 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 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. = 4.9 DEGREES REMARK 500 11 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 11 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 152 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 4 0.06 SIDE_CHAIN REMARK 500 1 G A 5 0.06 SIDE_CHAIN REMARK 500 2 G A 5 0.06 SIDE_CHAIN REMARK 500 2 A B 16 0.08 SIDE_CHAIN REMARK 500 3 G A 5 0.06 SIDE_CHAIN REMARK 500 3 A B 16 0.08 SIDE_CHAIN REMARK 500 4 A B 16 0.05 SIDE_CHAIN REMARK 500 5 G A 5 0.06 SIDE_CHAIN REMARK 500 6 G A 5 0.06 SIDE_CHAIN REMARK 500 7 G A 5 0.06 SIDE_CHAIN REMARK 500 7 A B 16 0.08 SIDE_CHAIN REMARK 500 8 A B 16 0.06 SIDE_CHAIN REMARK 500 10 G A 5 0.06 SIDE_CHAIN REMARK 500 10 G B 14 0.07 SIDE_CHAIN REMARK 500 10 A B 16 0.07 SIDE_CHAIN REMARK 500 10 G B 17 0.06 SIDE_CHAIN REMARK 500 11 G A 5 0.09 SIDE_CHAIN REMARK 500 11 A B 16 0.06 SIDE_CHAIN REMARK 500 11 G B 17 0.06 SIDE_CHAIN REMARK 500 13 G A 5 0.06 SIDE_CHAIN REMARK 500 16 A B 16 0.05 SIDE_CHAIN REMARK 500 17 G A 5 0.07 SIDE_CHAIN REMARK 500 17 G B 11 0.06 SIDE_CHAIN REMARK 500 18 A B 16 0.06 SIDE_CHAIN REMARK 500 22 G A 5 0.05 SIDE_CHAIN REMARK 500 22 G B 11 0.06 SIDE_CHAIN REMARK 500 22 A B 15 0.05 SIDE_CHAIN REMARK 500 23 G B 11 0.06 SIDE_CHAIN REMARK 500 23 G B 14 0.06 SIDE_CHAIN REMARK 500 23 A B 16 0.06 SIDE_CHAIN REMARK 500 24 G A 5 0.07 SIDE_CHAIN REMARK 500 24 G B 11 0.06 SIDE_CHAIN REMARK 500 26 G A 5 0.06 SIDE_CHAIN REMARK 500 26 G B 14 0.06 SIDE_CHAIN REMARK 500 26 A B 16 0.07 SIDE_CHAIN REMARK 500 29 G B 11 0.06 SIDE_CHAIN REMARK 500 29 A B 16 0.05 SIDE_CHAIN REMARK 500 30 G A 5 0.08 SIDE_CHAIN REMARK 500 30 G B 14 0.07 SIDE_CHAIN REMARK 500 31 G A 5 0.05 SIDE_CHAIN REMARK 500 31 A B 16 0.06 SIDE_CHAIN REMARK 500 32 G A 5 0.09 SIDE_CHAIN REMARK 500 33 G A 5 0.10 SIDE_CHAIN REMARK 500 33 A B 15 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1XV0 A 1 10 PDB 1XV0 1XV0 1 10 DBREF 1XV0 B 11 20 PDB 1XV0 1XV0 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 G C C P5P
MODRES 1XV0 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 1.61
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