HEADER RNA 24-MAY-10 2KYD TITLE RDC AND RCSA REFINEMENT OF AN A-FORM RNA: IMPROVEMENTS IN MAJOR GROOVE TITLE 2 WIDTH COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)- COMPND 3 3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS A-FORM RNA, SLB DUPLEX, MOLONEY MURINE LEUKEMIA VIRUS DIMERIZATION KEYWDS 2 SIGNAL, RDC AND RCSA REFINEMENT, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.S.TOLBERT,M.F.SUMMERS,Y.MIYAZAKI,S.BARTON,B.KINDE,P.STARK,R.SINGH, AUTHOR 2 A.BAX,D.CASE REVDAT 1 07-JUL-10 2KYD 0 JRNL AUTH B.S.TOLBERT,Y.MIYAZAKI,S.BARTON,B.KINDE,P.STARCK,R.SINGH, JRNL AUTH 2 A.BAX,D.A.CASE,M.F.SUMMERS JRNL TITL MAJOR GROOVE WIDTH VARIATIONS IN RNA STRUCTURES DETERMINED JRNL TITL 2 BY NMR AND IMPACT OF 13C RESIDUAL CHEMICAL SHIFT ANISOTROPY JRNL TITL 3 AND 1H-13C RESIDUAL DIPOLAR COUPLING ON REFINEMENT. JRNL REF J.BIOMOL.NMR V. 47 205 2010 JRNL REFN ISSN 0925-2738 JRNL PMID 20549304 JRNL DOI 10.1007/S10858-010-9424-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, D. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KYD COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-10. REMARK 100 THE RCSB ID CODE IS RCSB101727. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.25-1 MM RNA, 0.25 MM [U-100% REMARK 210 13C], [C-100% 13C] RNA, 0.25 MM REMARK 210 [G-100% 13C], [A-100% 13C] RNA, REMARK 210 150 MM SODIUM CHLORIDE, 10 MM REMARK 210 TRIS, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HMQC; 2D TR 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 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 C A 1 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 3 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 3 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 7 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A A 11 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 11 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A A 12 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 12 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 13 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 15 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 C B 17 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A B 19 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A B 19 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A B 19 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 A B 23 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A B 23 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A B 23 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 C B 25 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A B 27 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A B 27 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A B 27 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A B 28 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A B 28 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A B 28 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C B 29 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A B 31 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A B 31 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A B 31 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 C A 1 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 A A 3 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 A A 3 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 A A 7 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 A A 11 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A A 11 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 A A 12 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 12 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 720 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KYD A 1 16 PDB 2KYD 2KYD 1 16 DBREF 2KYD B 17 32 PDB 2KYD 2KYD 17 32 SEQRES 1 A 16 C U A G U U A G C U A A C SEQRES 2 A 16 U A G SEQRES 1 B 16 C U A G U U A G C U A A C SEQRES 2 B 16 U A G 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 139 0 0 0 0 0 0 6 0 0 0 4 END