10 20 30 40 50 60 70 80 2H49 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 23-MAY-06 2H49
TITLE THE NMR STRUCTURE OF AN INTERNAL LOOP FROM 23S RIBOSOMAL TITLE 2 RNA OF DEINOCOCCUS RADIODURANS DIFFERS FROM THE STRUCTURE TITLE 3 IN THE CRYSTAL OF THE RIBOSOMAL SUBUNIT
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*UP*AP*AP*GP*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED ON A DNA/RNA SYNTHESIZER; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED ON A DNA/RNA SYNTHESIZER
KEYWDS RNA INTERNAL LOOP 5'CUAAG3'/3'GAAGC5', COMPARISON BETWEEN KEYWDS 2 CRYSTAL STRUCTURE AND NMR STRUCTURE, THERMODYNAMICS OF KEYWDS 3 INTERNAL LOOP
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR N.SHANKAR
REVDAT 2 24-FEB-09 2H49 1 VERSN REVDAT 1 21-NOV-06 2H49 0
JRNL AUTH N.SHANKAR,S.D.KENNEDY,G.CHEN,T.R.KRUGH,D.H.TURNER JRNL TITL THE NMR STRUCTURE OF AN INTERNAL LOOP FROM 23S JRNL TITL 2 RIBOSOMAL RNA DIFFERS FROM ITS STRUCTURE IN JRNL TITL 3 CRYSTALS OF 50S RIBOSOMAL SUBUNITS. JRNL REF BIOCHEMISTRY V. 45 11776 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 17002278 JRNL DOI 10.1021/BI0605787
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 98 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SILICON GRAPHICS OCTANE COMPUTER, REMARK 3 AMBER 95 FORCE FIELD
REMARK 4 REMARK 4 2H49 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-06. REMARK 100 THE RCSB ID CODE IS RCSB037910.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 2MM TOTAL DUPLEX REMARK 210 CONCENTRATION; 80MM NACL, 10MM REMARK 210 SODIUM PHOSPHATE, 0.5MM REMARK 210 NA2EDTA, 90% H2O, 10% D2O; 2MM REMARK 210 TOTAL DUPLEX CONCENTRATION; REMARK 210 80MM NACL, 10MM SODIUM REMARK 210 PHOSPHATE, 0.5MM NA2EDTA, 100% REMARK 210 D2O 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 : SPARKY 3.110, NMRDRAW 2.3 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 U B 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 U B 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 U B 11 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 U B 11 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 4 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 U B 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 U B 11 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 6 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 6 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 U A 4 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 7 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 7 U B 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 7 C B 17 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 7 C B 18 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 8 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 8 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 8 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 8 U B 11 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 8 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 8 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 8 C B 18 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 9 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 9 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 9 U B 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 114 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 A A 8 0.07 SIDE_CHAIN REMARK 500 1 G B 10 0.06 SIDE_CHAIN REMARK 500 2 A A 8 0.07 SIDE_CHAIN REMARK 500 2 G B 10 0.06 SIDE_CHAIN REMARK 500 3 A A 8 0.07 SIDE_CHAIN REMARK 500 3 G B 10 0.06 SIDE_CHAIN REMARK 500 4 A A 8 0.08 SIDE_CHAIN REMARK 500 4 G B 10 0.06 SIDE_CHAIN REMARK 500 5 A A 8 0.08 SIDE_CHAIN REMARK 500 5 G B 10 0.06 SIDE_CHAIN REMARK 500 6 A A 8 0.05 SIDE_CHAIN REMARK 500 7 A A 8 0.08 SIDE_CHAIN REMARK 500 7 G B 10 0.06 SIDE_CHAIN REMARK 500 7 C B 17 0.06 SIDE_CHAIN REMARK 500 8 A A 8 0.08 SIDE_CHAIN REMARK 500 8 G B 10 0.06 SIDE_CHAIN REMARK 500 8 C B 17 0.07 SIDE_CHAIN REMARK 500 9 A A 5 0.06 SIDE_CHAIN REMARK 500 9 A A 8 0.08 SIDE_CHAIN REMARK 500 9 G B 10 0.06 SIDE_CHAIN REMARK 500 10 A A 5 0.06 SIDE_CHAIN REMARK 500 10 A A 8 0.06 SIDE_CHAIN REMARK 500 10 G B 10 0.06 SIDE_CHAIN REMARK 500 10 C B 17 0.07 SIDE_CHAIN REMARK 500 11 A A 8 0.06 SIDE_CHAIN REMARK 500 11 G B 10 0.06 SIDE_CHAIN REMARK 500 12 A A 8 0.06 SIDE_CHAIN REMARK 500 12 G B 10 0.06 SIDE_CHAIN REMARK 500 13 A A 8 0.06 SIDE_CHAIN REMARK 500 13 G B 10 0.06 SIDE_CHAIN REMARK 500 14 A A 8 0.07 SIDE_CHAIN REMARK 500 14 G B 10 0.06 SIDE_CHAIN REMARK 500 14 A B 15 0.06 SIDE_CHAIN REMARK 500 15 A A 8 0.07 SIDE_CHAIN REMARK 500 15 G B 10 0.06 SIDE_CHAIN REMARK 500 16 A A 8 0.07 SIDE_CHAIN REMARK 500 16 G B 10 0.06 SIDE_CHAIN REMARK 500 17 A A 8 0.06 SIDE_CHAIN REMARK 500 18 A A 8 0.08 SIDE_CHAIN REMARK 500 18 G B 10 0.06 SIDE_CHAIN REMARK 500 19 A A 8 0.06 SIDE_CHAIN REMARK 500 19 G B 10 0.06 SIDE_CHAIN REMARK 500 20 A A 8 0.06 SIDE_CHAIN REMARK 500 20 G B 10 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 2H49 A 1 9 PDB 2H49 2H49 1 9 DBREF 2H49 B 10 18 PDB 2H49 2H49 10 18
SEQRES 1 A 9 G G C U A A G A C SEQRES 1 B 9 G U C G A A G C C
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