HEADER RNA 01-JUL-08 2K5Z TITLE SOLUTION STRUCTURE AND DYNAMICS OF THE APICAL STEM-LOOP OF DUCK TITLE 2 HEPATITIS B VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUCK HBV APICAL LOOP; 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, DUCK, APICAL LOOP, EPSILON, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.A.M.AMPT,M.TESSARI,S.S.WIJMENGA REVDAT 3 16-MAR-22 2K5Z 1 REMARK REVDAT 2 17-NOV-09 2K5Z 1 JRNL REVDAT 1 14-JUL-09 2K5Z 0 JRNL AUTH K.A.AMPT,R.M.VAN DER WERF,F.H.NELISSEN,M.TESSARI, JRNL AUTH 2 S.S.WIJMENGA JRNL TITL THE UNSTABLE PART OF THE APICAL STEM OF DUCK HEPATITIS B JRNL TITL 2 VIRUS EPSILON SHOWS ENHANCED BASE PAIR OPENING BUT NOT PICO- JRNL TITL 3 TO NANOSECOND DYNAMICS AND IS ESSENTIAL FOR REVERSE JRNL TITL 4 TRANSCRIPTASE BINDING. JRNL REF BIOCHEMISTRY V. 48 10499 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19817488 JRNL DOI 10.1021/BI9011385 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.A.M.AMPT,O.M.OTTINK,F.C.GIRARD,F.H.T.NELISSEN,M.TESSARI, REMARK 1 AUTH 2 S.S.WIJMENGA REMARK 1 TITL 1H, 13C AND 15N NMR ASSIGNMENTS OF DUCK HBV APICAL STEM LOOP REMARK 1 TITL 2 OF THE EPSILON ENCAPSIDATION SIGNAL REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY, X-PLOR 3.851 REMARK 3 AUTHORS : GODDARD (SPARKY), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RDC REFINEMENT REMARK 4 REMARK 4 2K5Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100718. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 288; 298 REMARK 210 PH : 6.7; 6.7; 6.7 REMARK 210 IONIC STRENGTH : 10; 10; 10 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM DUCK HBV APICAL LOOP, 10 REMARK 210 MM SODIUM PHOSPHATE BUFFER, 0.1 REMARK 210 MM EDTA, 95% H2O, 5% D2O, 95% REMARK 210 H2O/5% D2O; 1.2 MM DUCK HBV REMARK 210 APICAL LOOP, 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER, 0.1 MM EDTA, REMARK 210 100% D2O, 100% D2O; 1 MM [U-13C; REMARK 210 U-15N]-URA DUCK HBV APICAL LOOP, REMARK 210 10 MM SODIUM PHOSPHATE BUFFER, REMARK 210 0.1 MM EDTA, 5% D2O, 95% H2O, 95% REMARK 210 H2O/5% D2O; 1 MM [U-13C; U-15N]- REMARK 210 URA DUCK HBV APICAL LOOP, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, 0.1 MM REMARK 210 EDTA, 100% D2O, 100% D2O; 0.7 MM REMARK 210 [U-13C; U-15N] DUCK HBV APICAL REMARK 210 LOOP, 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER, 0.1 MM EDTA, 5% D2O, 95% REMARK 210 H2O, 1 MM DSS, 95% H2O/5% D2O; REMARK 210 0.7 MM [U-13C; U-15N] DUCK HBV REMARK 210 APICAL LOOP, 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER, 0.1 MM EDTA, 5% REMARK 210 D2O, 95% H2O, 15 MG/ML PF1 REMARK 210 PHAGE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-13C NOESY; REMARK 210 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D DQF-COSY; 2D 1H-1H COSY; 3D REMARK 210 HCCH-TOCSY; 3D HCN REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, NMRDRAW, X-PLOR 3.851 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: 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 5 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 C A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 10 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OJ7 RELATED DB: PDB REMARK 900 UGUU TETRALOOP REMARK 900 RELATED ID: 2OJ8 RELATED DB: PDB REMARK 900 UGUU TETRALOOP CHEMICAL SHIFT REFINED REMARK 900 RELATED ID: 2K5Y RELATED DB: PDB REMARK 900 STRUCTURE BEFORE RDC REFINEMENT DBREF 2K5Z A 1 29 PDB 2K5Z 2K5Z 1 29 SEQRES 1 A 29 G G U C U A C A U U G C U SEQRES 2 A 29 G U U G U C G U G U G U G SEQRES 3 A 29 A 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 MODEL 1