HEADER RNA 28-MAY-08 2RPK TITLE SOLUTION STRUCTURE OF DOMAIN II OF THE POSITIVE POLARITY CCHMVD TITLE 2 HAMMERHEAD RIBOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS HAMMERHEAD RIBOZYME, VIROID, CCHMVD, HEXALOOP, RNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR J.GALLEGO,D.DUFOUR,M.DE LA PENA,S.GAGO,R.FLORES REVDAT 3 16-MAR-22 2RPK 1 REMARK REVDAT 2 03-MAR-09 2RPK 1 JRNL REVDAT 1 30-DEC-08 2RPK 0 JRNL AUTH D.DUFOUR,M.DE LA PENA,S.GAGO,R.FLORES,J.GALLEGO JRNL TITL STRUCTURE-FUNCTION ANALYSIS OF THE RIBOZYMES OF JRNL TITL 2 CHRYSANTHEMUM CHLOROTIC MOTTLE VIROID: A LOOP-LOOP JRNL TITL 3 INTERACTION MOTIF CONSERVED IN MOST NATURAL HAMMERHEADS JRNL REF NUCLEIC ACIDS RES. V. 37 368 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19043070 JRNL DOI 10.1093/NAR/GKN918 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, AMBER 8.0 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MINIMIZED AVERAGE STRUCTURE OF 33 REMARK 3 CONVERGED CONFORMERS WITH THE LEAST RESTRAINT VIOLATION ENERGY REMARK 3 AND TOTAL ENERGY REMARK 4 REMARK 4 2RPK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000150130. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 281; 296 REMARK 210 PH : 6; 6 REMARK 210 IONIC STRENGTH : 12.4; 12.4 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM RNA (5' REMARK 210 -R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)- REMARK 210 3'), 10 MM SODIUM PHOSPHATE, 0.1 MM EDTA, 90% H2O/10% D2O; 0.7 REMARK 210 MM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP* REMARK 210 CP*CP*C)-3'), 10 MM SODIUM PHOSPHATE, 0.1 MM EDTA, 100% D2O; 0.4 REMARK 210 MM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP* REMARK 210 UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 MM SODIUM PHOSPHATE, REMARK 210 0.1 MM EDTA, 90% H2O/10% D2O; 0.4 MM [U-100% 13C; U-100% 15N] REMARK 210 RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP* REMARK 210 CP*C)-3'), 10 MM SODIUM PHOSPHATE, 0.1 MM EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC; 3D 1H,13C HMQC- REMARK 210 NOESY; 3D HCCH-COSY; 2D HCCH- REMARK 210 TOCSY; 3D HCP; 3D 13C-ED-1H-31P REMARK 210 HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, SPARKY 3.110, AMBER REMARK 210 8.0 REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 RESTRAINED ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE STRUCTURE OF REMARK 210 33 CONVERGED CONFORMERS WITH THE REMARK 210 LEAST RESTRAINT VIOLATION ENERGY REMARK 210 AND TOTAL 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 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 A A 4 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 4 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 6 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 7 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 A A 8 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 8 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 A A 11 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 A A 13 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 A A 13 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 A A 13 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 A A 16 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 A A 16 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 16 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 C A 18 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 19 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 C A 20 N3 - C2 - O2 ANGL. DEV. = -5.0 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 A A 8 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RO2 RELATED DB: PDB DBREF 2RPK A 1 20 PDB 2RPK 2RPK 1 20 SEQRES 1 A 20 G G G A U C C A U G A C A SEQRES 2 A 20 G G A U C C C 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