10 20 30 40 50 60 70 80 2RO2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 05-MAR-08 2RO2
TITLE SOLUTION STRUCTURE OF DOMAIN I OF THE NEGATIVE POLARITY TITLE 2 CCHMVD HAMMERHEAD RIBOZYME
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP COMPND 4 *UP*CP*CP*C)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS HAMMERHEAD RIBOZYME, VIROID, CCHMVD, HEPTALOOP, RNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR J.GALLEGO,D.DUFOUR,S.GAGO,M.DE LA PENA,R.FLORES
REVDAT 2 03-MAR-09 2RO2 1 JRNL REVDAT 1 30-DEC-08 2RO2 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 JRNL TITL 4 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MINIMIZED AVERAGE STRUCTURE OF 29 REMARK 3 CONVERGED CONFORMERS WITH THE LEAST RESTRAINT VIOLATION ENERGY REMARK 3 AND TOTAL ENERGY
REMARK 4 REMARK 4 2RO2 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-08. REMARK 100 THE RCSB ID CODE IS RCSB150080.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 297; 281 REMARK 210 PH : 6; 6 REMARK 210 IONIC STRENGTH : 12.4; 12.4 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM RNA (5'-R(*GP*GP*GP*AP* REMARK 210 GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), REMARK 210 10MM SODIUM PHOSPHATE, 0.1MM EDTA, 100% D2O; 0.5MM RNA (5'-R(* REMARK 210 GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP* REMARK 210 CP*CP*C)-3'), 10MM SODIUM PHOSPHATE, 0.1MM EDTA, 90% H2O/10% REMARK 210 D2O; 1MM [U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP* REMARK 210 GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10MM SODIUM REMARK 210 PHOSPHATE, 0.1MM EDTA, 90% H2O/10% D2O; 0.5MM [U-100% 13C; U- REMARK 210 100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP* REMARK 210 UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10MM SODIUM PHOSPHATE, REMARK 210 0.1MM EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY, 2D 1H-1H REMARK 210 TOCSY, 2D DQF-COSY, 2D 1H-15N REMARK 210 HSQC, 2D HNN COSY, 2D 1H-13C REMARK 210 HSQC, 3D NOESY-HMQC, 3D HCCH REMARK 210 ECOSY, 2D HCCH-TOCSY, 3D HCP, REMARK 210 3D 13C-ED-1H-31P HETCOR, 3D REMARK 210 HCP-CCH TOCSY, 2D HCNCH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 700 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 REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 RESTRAINED ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS AND TOTAL 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 A A 4 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 4 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 4 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 A A 6 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 6 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 C A 7 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 C A 8 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 A A 11 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 A A 11 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 11 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 12 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 G A 13 C5' - C4' - O4' ANGL. DEV. = -7.8 DEGREES REMARK 500 G A 13 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 G A 13 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 G A 15 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 U A 18 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C A 21 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 22 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 C A 23 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 U A 9 0.06 SIDE_CHAIN REMARK 500 G A 10 0.12 SIDE_CHAIN REMARK 500 A A 12 0.10 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 2RO2 A 1 23 PDB 2RO2 2RO2 1 23
SEQRES 1 A 23 G G G A G A C C U G A A G SEQRES 2 A 23 U G G G U U 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