HEADER RNA 14-SEP-99 1D0T TITLE SOLUTION STRUCTURE OF A PHOSPHOROTHIOATE MODIFIED RNA TITLE 2 BINDING SITE FOR PHAGE MS2 COAT PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOROTHIOATE SUBSTITUTED PHAGE MS2 RNA COMPND 3 BINDING SITE; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: MS2 REPLICASE OPERATOR HAIRPIN. RP COMPND 7 PHOSPHORYL (NON-BRIDGING) SULFUR 5' TO EACH ADENINE COMPND 8 NUCLEOTIDE. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: TRANSCRIPTION BY T7 RNA PLOYMERASE USING 5'- SOURCE 4 A-THIO-ATP KEYWDS RNA HAIRPIN, PHOSPHOROTHIOATE, THIOPHOSPHATE, BULGED BASE, KEYWDS 2 STEM-LOOP EXPDTA SOLUTION NMR NUMMDL 10 MDLTYP MINIMIZED AVERAGE AUTHOR J.S.SMITH,E.P.NIKONOWICZ REVDAT 2 24-FEB-09 1D0T 1 VERSN REVDAT 1 24-MAY-00 1D0T 0 JRNL AUTH J.S.SMITH,E.P.NIKONOWICZ JRNL TITL PHOSPHOROTHIOATE SUBSTITUTION CAN SUBSTANTIALLY JRNL TITL 2 ALTER RNA CONFORMATION. JRNL REF BIOCHEMISTRY V. 39 5642 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10801314 JRNL DOI 10.1021/BI992712B REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED USING 313 REMARK 3 CONFORMATIONALLY RESTRICTIVE NOE DISTANCE CONSTRAINTS (I.E., REMARK 3 INTRA-RESIDUE SUGAR-SUGAR NOES ARE NOT INCLUDED), 20 H-BOND REMARK 3 BASE PAIR CONSTRAINTS, 30 BACKBONE DIHEDRAL RESTRAINTS, AND REMARK 3 DIHEDRAL RESTRAINTS TO RESTRICT SUGAR PUCKER CONFORMATION. REMARK 3 PARAMETER FILE WAS MODIFIED TO INCORPORATE BOND-LENGTH, BOND- REMARK 3 ANGLE, CHARGE, VAN DER WAAL'S RADIUS FOR THE RP PHOSPHORYL REMARK 3 SULFUR ATOMS LOCATED 5' TO EACH ADENINE IN THE SEQUENCE. REMARK 3 [JAROSZEWSKI, JW., ET AL., ANTI-CANCER DRUG DESIGN (1992) 7, REMARK 3 253; FLORIAN, J. ET AL., J. AM. CHEM. SOC. (1998) 120, 7959]. REMARK 4 REMARK 4 1D0T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-99. REMARK 100 THE RCSB ID CODE IS RCSB009692. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : ~50MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0 MM REPLICASE OPERATOR RNA REMARK 210 U-15N,13C AT U, C, AND G, REMARK 210 UNLABELED A; PHOSPHOROTHIOATE REMARK 210 5' TO EACH ADENINE;; 10 MM KPI REMARK 210 BUFFER; 10 MM NACL; 0.2 MM REMARK 210 EDTA; 2.0 MM REPLICASE REMARK 210 OPERATOR RNA U-15N,13C AT U, REMARK 210 C, AND G, UNLABELED A; REMARK 210 PHOSPHOROTHIOATE 5' TO EACH REMARK 210 ADENINE;; 10 MM KPI BUFFER; 10 REMARK 210 MM NACL; 0.2 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D_15N-SEPARATED_ REMARK 210 NOESY, DQF-COSY, 31P-1H REMARK 210 HETCOR, 2D 13C-FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR 1994, FELIX 1998, X- REMARK 210 PLOR 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 MOLECULAR DYNAMICS REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM,STRUCTURES WITH REMARK 210 ACCEPTABLE COVALENT GEOMETRY, REMARK 210 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: THE STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR AND 2D/3D HETERONUCLEAR TECHNIQUES. FILTERED REMARK 210 EXPERIMENTS USED TO IDENTIFY INTER-RESIDUE NOES INVOLVING REMARK 210 UNLABELED A RESIDUES 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 4 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 4 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 5 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 120 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D0U RELATED DB: PDB REMARK 900 PHAGE MS2 REPLICASE OPERATOR RNA HAIRPIN DBREF 1D0T A 1 21 PDB 1D0T 1D0T 1 21 SEQRES 1 A 21 G G G SRA U C SRA C C SRA U U SRA SEQRES 2 A 21 G G G SRA U C U C MODRES 1D0T SRA A 4 A ADENOSINE -5'-THIO-MONOPHOSPHATE MODRES 1D0T SRA A 7 A ADENOSINE -5'-THIO-MONOPHOSPHATE MODRES 1D0T SRA A 10 A ADENOSINE -5'-THIO-MONOPHOSPHATE MODRES 1D0T SRA A 13 A ADENOSINE -5'-THIO-MONOPHOSPHATE MODRES 1D0T SRA A 17 A ADENOSINE -5'-THIO-MONOPHOSPHATE HET SRA A 4 33 HET SRA A 7 33 HET SRA A 10 33 HET SRA A 13 33 HET SRA A 17 33 HETNAM SRA ADENOSINE -5'-THIO-MONOPHOSPHATE FORMUL 1 SRA 5(C10 H14 N5 O6 P S) LINK P SRA A 4 O3' G A 3 1555 1555 1.61 LINK O3' SRA A 4 P U A 5 1555 1555 1.61 LINK P SRA A 7 O3' C A 6 1555 1555 1.61 LINK O3' SRA A 7 P C A 8 1555 1555 1.61 LINK P SRA A 10 O3' C A 9 1555 1555 1.61 LINK O3' SRA A 10 P U A 11 1555 1555 1.61 LINK P SRA A 13 O3' U A 12 1555 1555 1.61 LINK O3' SRA A 13 P G A 14 1555 1555 1.61 LINK P SRA A 17 O3' G A 16 1555 1555 1.61 LINK O3' SRA A 17 P U A 18 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 152 0 5 0 0 0 0 6 0 0 0 2 END