10 20 30 40 50 60 70 80 2OJ7 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 12-JAN-07 2OJ7
TITLE NMR STRUCTURE OF THE UGUU TETRALOOP OF DUCK EPSILON APICAL TITLE 2 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 SOURCE 4 DUCK HEPATITIS B VIRUS
KEYWDS HBV, RNA, EPSILON, DUCK, NMR, UGUU, TETRALOOP
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR F.C.GIRARD,O.M.OTTINK,K.A.M.AMPT,M.TESSARI,S.S.WIJMENGA
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, JRNL AUTH 2 S.S.WIJMENGA JRNL TITL THERMODYNAMICS AND NMR STUDIES ON DUCK, HERON AND JRNL TITL 2 HUMAN HBV 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : STEIN, E.G. RICE L.M. AND BRUNGER A.T. 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 RCSB ID CODE IS RCSB041202.
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, REMARK 210 95% H2O, 5% D2O; 1.0 MM 13C/ REMARK 210 15N/2H-U LABELED RNA, 10MM NA REMARK 210 PHOSPHATE BUFFER, PH 6.7, 0.1 REMARK 210 MM EDTA, 95% H2O, 5% D2O; 1.2 REMARK 210 MM RNA, 10MM NA PHOSPHATE REMARK 210 BUFFER, PH 6.7, 0.1 MM EDTA, REMARK 210 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, REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, HMQC-15N/1H, DQF- REMARK 210 COSY, 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 : X-PLOR 3.851 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 REMARK 210 SPECTRA 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 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. = 4.6 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -3.1 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. = 4.9 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