HEADER RNA 02-JAN-09 2KD4 TITLE SOLUTION STRUCTURE AND THERMODYNAMICS OF 2',5' RNA TITLE 2 INTERCALATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC 2',5' RNA KEYWDS PROFLAVINE, NMR, INTERCALATION, 2',5' RNA, RNA, NEAREST- KEYWDS 2 NEIGHBOR EXCLUSION EXPDTA SOLUTION NMR AUTHOR E.D.HOROWITZ,S.LILAVIVAT,B.W.HOLLADAY,M.W.GERMANN,N.V.HUD REVDAT 2 19-MAY-09 2KD4 1 JRNL REVDAT 1 07-APR-09 2KD4 0 JRNL AUTH E.D.HOROWITZ,S.LILAVIVAT,B.W.HOLLADAY,M.W.GERMANN, JRNL AUTH 2 N.V.HUD JRNL TITL SOLUTION STRUCTURE AND THERMODYNAMICS OF 2',5' RNA JRNL TITL 2 INTERCALATION. JRNL REF J.AM.CHEM.SOC. V. 131 5831 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19309071 JRNL DOI 10.1021/JA810068E REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 300 RANDOM STRUCTURES WERE GENERATED REMARK 3 AND ANNEALED. THE LOWEST 10 ENERGY STRUCTURES WERE THEN RE- REMARK 3 ANNEALED REMARK 4 REMARK 4 2KD4 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB100971. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 282; 282 REMARK 210 PH : 6.5; NULL REMARK 210 IONIC STRENGTH : 260; 130 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM 2',5' RNA-1, 4 MM REMARK 210 PROFLAVINE-2, 60 MM SODIUM REMARK 210 PHOSPHATE-3, 200 MM SODIUM REMARK 210 CHLORIDE-4, 99.9% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-1H NOESY; 31P-1H HETCOR; REMARK 210 1H-1H TOCSY; 31P-DECOUPLED 1H- REMARK 210 1H COSY; 1H-1H NOESY WITH REMARK 210 WATERGATE WATER SUPPRESSION REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, SPARKY, AMBER REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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 G A 1 O4' - C4' - C3' ANGL. DEV. = 7.3 DEGREES REMARK 500 G A 1 C5' - C4' - O4' ANGL. DEV. = 5.5 DEGREES REMARK 500 G A 1 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 C A 2 O4' - C4' - C3' ANGL. DEV. = 7.1 DEGREES REMARK 500 C A 2 C3' - C2' - C1' ANGL. DEV. = 6.1 DEGREES REMARK 500 C A 2 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 C A 2 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 C A 5 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 7 O5' - C5' - C4' ANGL. DEV. = 13.7 DEGREES REMARK 500 G A 7 C5' - C4' - C3' ANGL. DEV. = -10.4 DEGREES REMARK 500 G A 7 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 C A 8 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 C A 8 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 C A 8 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES REMARK 500 C A 8 C6 - N1 - C1' ANGL. DEV. = -7.6 DEGREES REMARK 500 C A 8 C2 - N1 - C1' ANGL. DEV. = 8.1 DEGREES REMARK 500 G B 1 O4' - C4' - C3' ANGL. DEV. = 6.9 DEGREES REMARK 500 G B 1 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 C B 2 O4' - C4' - C3' ANGL. DEV. = 6.9 DEGREES REMARK 500 C B 2 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES REMARK 500 C B 2 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 C B 2 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 G B 6 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 G B 7 O4' - C1' - N9 ANGL. DEV. = -6.0 DEGREES REMARK 500 C B 8 C5' - C4' - O4' ANGL. DEV. = 6.5 DEGREES REMARK 500 C B 8 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 C B 8 C6 - N1 - C1' ANGL. DEV. = -7.8 DEGREES REMARK 500 C B 8 C2 - N1 - C1' ANGL. DEV. = 8.0 DEGREES 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 G A 1 0.08 SIDE_CHAIN REMARK 500 C A 2 0.12 SIDE_CHAIN REMARK 500 G A 4 0.13 SIDE_CHAIN REMARK 500 G A 6 0.15 SIDE_CHAIN REMARK 500 G A 7 0.09 SIDE_CHAIN REMARK 500 G B 1 0.07 SIDE_CHAIN REMARK 500 C B 2 0.12 SIDE_CHAIN REMARK 500 G B 4 0.12 SIDE_CHAIN REMARK 500 G B 6 0.12 SIDE_CHAIN REMARK 500 G B 7 0.13 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PRL B 17 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PRL A 17 DBREF 2KD4 A 1 8 PDB 2KD4 2KD4 1 8 DBREF 2KD4 B 1 8 PDB 2KD4 2KD4 1 8 SEQRES 1 A 8 G C C G C G G C SEQRES 1 B 8 G C C G C G G C HET PRL B 17 28 HET PRL A 17 28 HETNAM PRL PROFLAVIN FORMUL 3 PRL 2(C13 H11 N3) LINK O2' G A 1 P C A 2 1555 1555 1.61 LINK O2' C A 2 P C A 3 1555 1555 1.60 LINK O2' C A 3 P G A 4 1555 1555 1.63 LINK O2' G A 4 P C A 5 1555 1555 1.60 LINK O2' C A 5 P G A 6 1555 1555 1.61 LINK O2' G A 6 P G A 7 1555 1555 1.62 LINK O2' G A 7 P C A 8 1555 1555 1.60 LINK O2' G B 1 P C B 2 1555 1555 1.61 LINK O2' C B 2 P C B 3 1555 1555 1.61 LINK O2' C B 3 P G B 4 1555 1555 1.61 LINK O2' G B 4 P C B 5 1555 1555 1.60 LINK O2' C B 5 P G B 6 1555 1555 1.61 LINK O2' G B 6 P G B 7 1555 1555 1.60 LINK O2' G B 7 P C B 8 1555 1555 1.60 SITE 1 AC1 5 G A 4 C A 5 G A 6 C B 3 SITE 2 AC1 5 G B 4 SITE 1 AC2 5 C A 2 C A 3 G A 4 C B 5 SITE 2 AC2 5 G B 6 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 MASTER 135 0 2 0 0 0 4 6 0 0 0 2 END