HEADER RNA 23-MAY-06 2H49 TITLE THE NMR STRUCTURE OF AN INTERNAL LOOP FROM 23S RIBOSOMAL RNA OF TITLE 2 DEINOCOCCUS RADIODURANS DIFFERS FROM THE STRUCTURE IN THE CRYSTAL OF TITLE 3 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 CRYSTAL KEYWDS 2 STRUCTURE AND NMR STRUCTURE, THERMODYNAMICS OF INTERNAL LOOP, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.SHANKAR REVDAT 3 09-MAR-22 2H49 1 REMARK 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 RIBOSOMAL RNA JRNL TITL 2 DIFFERS FROM ITS STRUCTURE IN CRYSTALS OF 50S RIBOSOMAL JRNL TITL 3 SUBUNITS. JRNL REF BIOCHEMISTRY V. 45 11776 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 17002278 JRNL DOI 10.1021/BI0605787 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY 3.110, DISCOVER 98 REMARK 3 AUTHORS : T. D. GODDARD AND D. G. KNELLER (SPARKY), REMARK 3 MOLECULAR SIMULATIONS INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SILICON GRAPHICS OCTANE COMPUTER,AMBER REMARK 3 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 DEPOSITION ID IS D_1000037910. 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 CONCENTRATION; REMARK 210 80MM NACL, 10MM SODIUM PHOSPHATE, REMARK 210 0.5MM NA2EDTA, 90% H2O, 10% D2O; REMARK 210 2MM TOTAL DUPLEX CONCENTRATION; REMARK 210 80MM NACL, 10MM SODIUM PHOSPHATE, REMARK 210 0.5MM NA2EDTA, 100% 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 : NMRDRAW 2.3 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, RESTRAINED MOLECULAR REMARK 210 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,STRUCTURES REMARK 210 WITH THE LOWEST 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 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 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. = 4.8 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. = 5.5 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. = 4.7 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 MODEL 1