HEADER RNA 12-OCT-09 2KPD TITLE STRUCTURE DETERMINATION OF THE TOP-LOOP OF THE CONSERVED 3 TERMINAL TITLE 2 SECONDARY STRUCTURE IN THE GENOME OF YFV-MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*UP*GP*AP*GP*CP*UP*CP*AP*GP*UP*UP*UP*GP*CP*UP*CP*A)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS YELLOW FEVER VIRUS MUTANT, 3'-TERMINAL LOOP, GENOME, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.LESCRINIER,N.DYUBANKOVA,K.NAUWELAERTS,R.JONES,P.HERDEWIJN REVDAT 2 14-JUL-10 2KPD 1 JRNL REVDAT 1 30-JUN-10 2KPD 0 JRNL AUTH E.LESCRINIER,N.DYUBANKOVA,K.NAUWELAERTS,R.JONES,P.HERDEWIJN JRNL TITL STRUCTURE DETERMINATION OF THE TOP-LOOP OF THE CONSERVED JRNL TITL 2 3'-TERMINAL SECONDARY STRUCTURE IN THE GENOME OF JRNL TITL 3 FLAVIVIRUSES. JRNL REF CHEMBIOCHEM V. 11 1404 2010 JRNL REFN ISSN 1439-4227 JRNL PMID 20540055 JRNL DOI 10.1002/CBIC.200900765 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, C.D. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN WATER BOX REMARK 4 REMARK 4 2KPD COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB101406. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295; 283 REMARK 210 PH : 5.0; 5.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MM RNA, 100% D2O; 1-2 MM REMARK 210 RNA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY; 2D 1H-1H NOESY; 2D REMARK 210 1H-31P-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H61 A A 3 O4 U A 15 1.42 REMARK 500 O6 G A 4 H41 C A 14 1.45 REMARK 500 O6 G A 2 H41 C A 16 1.48 REMARK 500 H1 G A 4 N3 C A 14 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 5 A A 3 C4 A A 3 C5 -0.043 REMARK 500 8 A A 3 N3 A A 3 C4 0.039 REMARK 500 REMARK 500 REMARK: NULL 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 4 A A 3 N1 - C2 - N3 ANGL. DEV. = -3.4 DEGREES REMARK 500 5 A A 3 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 A A 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 A A 3 N1 - C2 - N3 ANGL. DEV. = -3.0 DEGREES REMARK 500 8 A A 3 N1 - C2 - N3 ANGL. DEV. = -3.0 DEGREES REMARK 500 10 C A 5 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KPC RELATED DB: PDB DBREF 2KPD A 1 17 PDB 2KPD 2KPD 1 17 SEQRES 1 A 17 U G A G C U C A G U U U G SEQRES 2 A 17 C U C A 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 109 0 0 0 0 0 0 6 0 0 0 2 END