HEADER RNA 24-SEP-02 1MV2 TITLE THE TANDEM, FACE-TO-FACE AP PAIRS IN 5'(RGGCAPGCCU)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*AP*(P5P)P*GP*CP*CP*U)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RIBONUCLEIC ACID, DUPLEX, TANDEM MISMATCH, PURINE, RNA EXPDTA SOLUTION NMR AUTHOR B.M.ZNOSKO,M.E.BURKARD,T.R.KRUGH,D.H.TURNER REVDAT 4 22-MAY-24 1MV2 1 REMARK REVDAT 3 23-FEB-22 1MV2 1 REMARK LINK REVDAT 2 24-FEB-09 1MV2 1 VERSN REVDAT 1 18-DEC-02 1MV2 0 JRNL AUTH B.M.ZNOSKO,M.E.BURKARD,T.R.KRUGH,D.H.TURNER JRNL TITL MOLECULAR RECOGNITION IN PURINE-RICH INTERNAL LOOPS: JRNL TITL 2 THERMODYNAMIC, STRUCTURAL, AND DYNAMIC CONSEQUENCES OF JRNL TITL 3 PURINE FOR ADENINE SUBSTITUTIONS IN 5'(RGGCAAGCCU)2 JRNL REF BIOCHEMISTRY V. 41 14978 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12475247 JRNL DOI 10.1021/BI0203278 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.M.ZNOSKO,M.E.BURKARD,S.J.SCHROEDER,T.R.KRUGH,D.H.TURNER REMARK 1 TITL SHEARED AANTI-AANTI BASE PAIRS IN A DESTABILIZING 2X2 REMARK 1 TITL 2 INTERNAL LOOP: THE NMR STRUCTURE OF 5'(RGGCAAGCCU)2 REMARK 1 REF BIOCHEMISTRY V. 41 14969 2002 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI020326F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 5.2, DISCOVER 95.0 REMARK 3 AUTHORS : VARIAN (VNMR), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF 71 REMARK 3 INTERPROTON DISTANCE RESTRAINTS PER STRAND, 18 HYDROGEN BOND REMARK 3 RESTRAINTS, AND 59 DIHEDRAL ANGLE RESTRAINTS PER STRAND. REMARK 4 REMARK 4 1MV2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017206. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 303 REMARK 210 PH : 6.5; 7.7 REMARK 210 IONIC STRENGTH : 90% H2O, 10% D2O; 99.996% D2O REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM RNA, 80 MM NACL, 10MM REMARK 210 PHOSPHATE BUFFER, 0.5MM EDTA; 90% REMARK 210 H2O, 10% D2O; 2MM RNA, 80 MM REMARK 210 NACL, 10MM PHOSPHATE BUFFER, REMARK 210 0.5MM EDTA; 99.996% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, DISCOVER 95.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 A A 4 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 7 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 C B 8 O4' - C1' - N1 ANGL. DEV. = 4.7 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 6 0.06 SIDE CHAIN REMARK 500 G B 6 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YFV RELATED DB: PDB REMARK 900 1YFV IS TANDEM, SHEARED GA PAIRS IN THE SAME STEM, DETERMINED BY 2D REMARK 900 NMR REMARK 900 RELATED ID: 1GID RELATED DB: PDB REMARK 900 1GID IS TANDEM, SHEARED AA PAIRS IN THE J4/5 LOOP OF TETRAHYMENA REMARK 900 THERMOPHILA, DETERMINED BY X-RAY CRYSTALLOGRAPHY REMARK 900 RELATED ID: 1MUV RELATED DB: PDB REMARK 900 1MUV IS THE TANDEM, SHEARED AA PAIRS, IN 5'(RGGCAAGCCU)2 REMARK 900 RELATED ID: 1MV1 RELATED DB: PDB REMARK 900 1MV1 IS THE TANDEM, SHEARED PA PAIRS IN 5'(RGGCPAGCCU)2 REMARK 900 RELATED ID: 1MV6 RELATED DB: PDB REMARK 900 1MV6 IS THE TANDEM, SHEARED PP PAIRS IN 5'(RGGCPPGCCU)2 DBREF 1MV2 A 1 9 PDB 1MV2 1MV2 1 9 DBREF 1MV2 B 1 9 PDB 1MV2 1MV2 1 9 SEQRES 1 A 9 G G C A P5P G C C U SEQRES 1 B 9 G G C A P5P G C C U MODRES 1MV2 P5P A 5 A PURINE RIBOSIDE-5'-MONOPHOSPHATE MODRES 1MV2 P5P B 5 A PURINE RIBOSIDE-5'-MONOPHOSPHATE HET P5P A 5 31 HET P5P B 5 31 HETNAM P5P PURINE RIBOSIDE-5'-MONOPHOSPHATE FORMUL 1 P5P 2(C10 H13 N4 O7 P) LINK O3' A A 4 P P5P A 5 1555 1555 1.62 LINK O3' P5P A 5 P G A 6 1555 1555 1.62 LINK O3' A B 4 P P5P B 5 1555 1555 1.62 LINK O3' P5P B 5 P G B 6 1555 1555 1.62 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