HEADER RNA 12-JAN-07 2OJ7 TITLE NMR STRUCTURE OF THE UGUU TETRALOOP OF DUCK EPSILON APICAL STEM LOOP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(P*GP*CP*UP*GP*UP*UP*GP*U)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE OF THIS RNA CAN BE FOUND IN DUCK SOURCE 4 HEPATITIS B VIRUS KEYWDS HBV, RNA, EPSILON, DUCK, UGUU, TETRALOOP EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.C.GIRARD,O.M.OTTINK,K.A.M.AMPT,M.TESSARI,S.S.WIJMENGA REVDAT 4 27-DEC-23 2OJ7 1 REMARK REVDAT 3 16-MAR-22 2OJ7 1 REMARK REVDAT 2 24-FEB-09 2OJ7 1 VERSN REVDAT 1 22-MAY-07 2OJ7 0 JRNL AUTH F.C.GIRARD,O.M.OTTINK,K.A.AMPT,M.TESSARI,S.S.WIJMENGA JRNL TITL THERMODYNAMICS AND NMR STUDIES ON DUCK, HERON AND HUMAN HBV JRNL TITL 2 ENCAPSIDATION SIGNALS. JRNL REF NUCLEIC ACIDS RES. V. 35 2800 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17430968 JRNL DOI 10.1093/NAR/GKM131 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851 REMARK 3 AUTHORS : STEIN, E.G. RICE L.M. AND BRUNGER A.T. (X-PLOR), REMARK 3 STEIN, E.G. RICE L.M. AND BRUNGER A.T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OJ7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041202. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 5; 15; 25 REMARK 210 PH : 6.7; 6.7; 6.7 REMARK 210 IONIC STRENGTH : 10 MM; 10 MM; 10 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM RNA, 10MM NA PHOSPHATE REMARK 210 BUFFER, PH 6.7, 0.1 MM EDTA, 95% REMARK 210 H2O, 5% D2O; 1.0 MM 13C/15N/2H-U REMARK 210 LABELED RNA, 10MM NA PHOSPHATE REMARK 210 BUFFER, PH 6.7, 0.1 MM EDTA, 95% REMARK 210 H2O, 5% D2O; 1.2 MM RNA, 10MM NA REMARK 210 PHOSPHATE BUFFER, PH 6.7, 0.1 MM REMARK 210 EDTA, D2O; 1.0 MM 13C/15N/2H-U REMARK 210 LABELED RNA, 10MM NA PHOSPHATE REMARK 210 BUFFER, PH 6.7, 0.1 MM EDTA, D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HMQC-15N/1H; DQF-COSY; REMARK 210 HMQC-13C/1H REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS USING REMARK 210 XPLOR 3.851 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 800 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: IN ADDITION TOCSY SPECTRA AND 31P 1D AND 31P HMBC SPECTRA REMARK 210 WERE RECORDED. 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 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 14 C3' - C2' - C1' ANGL. DEV. = 4.9 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. = -3.0 DEGREES REMARK 500 1 U A 15 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U A 16 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 U A 13 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 2 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 14 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 U A 15 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 2 U A 16 C3' - C2' - C1' ANGL. DEV. = 5.3 DEGREES REMARK 500 2 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 3 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 G A 14 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 3 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 14 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 U A 15 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 3 U A 16 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 3 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 G A 17 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 4 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 4 G A 14 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 4 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 14 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 U A 15 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 4 U A 16 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 4 G A 17 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 17 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 5 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 5 G A 14 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 5 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 G A 14 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 5 U A 15 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 5 U A 16 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 5 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 6 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 G A 14 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 6 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 91 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2OJ7 A 11 18 PDB 2OJ7 2OJ7 11 18 SEQRES 1 A 8 G C U G U U G U 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