2K5Z - Header Asymmetric Unit

HEADER RNA 01-JUL-08 2K5Z

TITLE SOLUTION STRUCTURE AND DYNAMICS OF THE APICAL STEM-LOOP OF TITLE 2 DUCK 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 SOURCE 4 DUCK 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 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 JRNL TITL 2 HEPATITIS B VIRUS EPSILON SHOWS ENHANCED BASE PAIR JRNL TITL 3 OPENING BUT NOT PICO- TO NANOSECOND DYNAMICS AND IS JRNL TITL 4 ESSENTIAL FOR REVERSE 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, REMARK 1 AUTH 2 M.TESSARI,S.S.WIJMENGA REMARK 1 TITL 1H, 13C AND 15N NMR ASSIGNMENTS OF DUCK HBV APICAL REMARK 1 TITL 2 STEM LOOP 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 : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RDC REFINEMENT

REMARK 4 REMARK 4 2K5Z COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-08. REMARK 100 THE RCSB ID CODE IS RCSB100718.

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, REMARK 210 10 MM SODIUM PHOSPHATE BUFFER, REMARK 210 0.1 MM EDTA, 95% H2O, 5% D2O, REMARK 210 95% H2O/5% D2O; 1.2 MM DUCK REMARK 210 HBV APICAL LOOP, 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER, 0.1 MM EDTA, REMARK 210 100% D2O, 100% D2O; 1 MM [U- REMARK 210 13C; U-15N]-URA DUCK HBV REMARK 210 APICAL LOOP, 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER, 0.1 MM EDTA, REMARK 210 5% D2O, 95% H2O, 95% H2O/5% REMARK 210 D2O; 1 MM [U-13C; U-15N]-URA REMARK 210 DUCK HBV APICAL LOOP, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, 0.1 REMARK 210 MM EDTA, 100% D2O, 100% 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, REMARK 210 5% D2O, 95% H2O, 1 MM DSS, 95% REMARK 210 H2O/5% D2O; 0.7 MM [U-13C; U- REMARK 210 15N] DUCK HBV APICAL LOOP, 10 REMARK 210 MM SODIUM PHOSPHATE BUFFER, REMARK 210 0.1 MM EDTA, 5% D2O, 95% H2O, REMARK 210 15 MG/ML PF1 PHAGE, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-13C REMARK 210 NOESY; 2D 1H-15N HSQC; 2D 1H- REMARK 210 13C HSQC; 2D DQF-COSY; 2D 1H- REMARK 210 1H COSY; 3D 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 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