HEADER RNA 04-AUG-98 17RA TITLE BRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 COAT TITLE 2 PROTEINS, NMR, 12 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RBS AND START SITE FOR PHAGE GA REPLICASE GENE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO SYNTHESIS FROM DNA TEMPLATE USING T7 RNA SOURCE 4 POLYMERASE. HAIRPIN CORRESPONDS TO NT -16 - +5 OF PHAGE GA REPLICASE SOURCE 5 AND THE YEAST PRE-MRNA BRANCHPOINT HELIX KEYWDS BRANCHPOINT HELIX, PHAGE MS2, BULGE, BASE TRIPLE, RIBONUCLEIC ACID, KEYWDS 2 RNA EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR E.P.NIKONOWICZ,J.S.SMITH REVDAT 4 22-MAY-24 17RA 1 REMARK REVDAT 3 16-FEB-22 17RA 1 REMARK REVDAT 2 24-FEB-09 17RA 1 VERSN REVDAT 1 20-APR-99 17RA 0 JRNL AUTH J.S.SMITH,E.P.NIKONOWICZ JRNL TITL NMR STRUCTURE AND DYNAMICS OF AN RNA MOTIF COMMON TO THE JRNL TITL 2 SPLICEOSOME BRANCH-POINT HELIX AND THE RNA-BINDING SITE FOR JRNL TITL 3 PHAGE GA COAT PROTEIN. JRNL REF BIOCHEMISTRY V. 37 13486 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9753434 JRNL DOI 10.1021/BI981558A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 17RA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170178. 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 : 20 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 10% H2O/90% D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D/3D NOESY; COSY; HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 950 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 75 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: FURTHER DETAILS OF DATA ACQUISITION AND STRUCTURE REMARK 210 CALCULATION CAN BE FOUND IN THE METHODS SECTION OF THE REMARK 210 MANUSCRIPT LISTED ABOVE. MODELS 1-6 ARE MINIMIZED STRUCTURES REMARK 210 CALCULATED WITHOUT BASE PAIR CONSTRAINTS FOR A6, A7, AND U16. REMARK 210 MODELS 7-12 ARE MINIMIZED STRUCTURES CALCULATED USING A6-U16 REMARK 210 BASE PAIR CONSTRAINTS AND AN A7 N1H-U16 O2 HYDROGEN BOND. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 A A 6 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 7 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 9 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 10 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 13 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 17 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 19 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 A A 6 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 2 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 7 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 9 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 17 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 19 C8 - N9 - C4 ANGL. DEV. = -3.0 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. = -3.0 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 3 A A 6 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 3 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 254 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AAU REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: A-A)*U MOTIF. PKA OF A7~6.1 AND IS PARTIALLY REMARK 800 PROTONATED AT PH 6.8, A7 NH1 MAY BE STABILIZED BY U16 O2 (MODELS REMARK 800 7-12). DBREF 17RA A 1 21 PDB 17RA 17RA 1 21 SEQRES 1 A 21 G G C G U A A G G A U U A SEQRES 2 A 21 C C U A U G C C SITE 1 AAU 3 A A 6 A A 7 U A 16 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