HEADER RNA 20-APR-04 1T28 TITLE HIGH RESOLUTION STRUCTURE OF A PICORNAVIRAL INTERNAL CIS- TITLE 2 ACTING REPLICATION ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 34-MER; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CRE OF THE HUMAN RHINOVIRUS TYPE 14; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: MINIMAL FUNCTIONAL SEQUENCE OF HRV-14 CRE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE RNA SEQUENCE WAS SYNTHESIZED USING T7 SOURCE 4 SYSTEM. THE SEQUENCE OCCURS IN HUMAN RHINOVIRUS TYPE 14. KEYWDS CRE, PICORNAVIRUS, RHINO VIRUS, STEM LOOP EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR V.THIVIYANATHAN,Y.YANG,K.KALUARACHCHI,R.REYNBRAND, AUTHOR 2 D.G.GORENSTEIN,S.M.LEMON REVDAT 3 24-FEB-09 1T28 1 VERSN REVDAT 2 07-SEP-04 1T28 1 JRNL REVDAT 1 10-AUG-04 1T28 0 JRNL AUTH V.THIVIYANATHAN,Y.YANG,K.KALUARACHCHI,R.REYNBRAND, JRNL AUTH 2 D.G.GORENSTEIN,S.M.LEMON JRNL TITL HIGH RESOLUTION STRUCTURE OF A PICORNAVIRAL JRNL TITL 2 INTERNAL CIS-ACTING REPLICATION ELEMENT(CRE). JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 12688 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15314212 JRNL DOI 10.1073/PNAS.0403079101 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER, A.T., ET AL., REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T28 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-04. REMARK 100 THE RCSB ID CODE IS RCSB022219. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298 REMARK 210 PH : 6.8; 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 1.4 MM RNA U-15N,13C, 10 MM REMARK 210 PHOSPHATE BUFFER (PH 6.8), 10 REMARK 210 MM KCL, 0.02 MM EDTA, 90% H2O, REMARK 210 10% D2O; 1.8 MM RNA, 8-10 MM REMARK 210 PHOSPHATE BUFFER (PH 6.8), 10 REMARK 210 MM KCL, 0.02 MM EDTA, 90% H2O, REMARK 210 10% D2O; 1.8 MM RNA, 8-10 MM REMARK 210 PHOSPHATE BUFFER (PH 6.8), 10 REMARK 210 MM KCL, 0.4-4 MM MG2+, 90% REMARK 210 H2O, 10% D2O; 0.8 MM RNA, 15N, REMARK 210 13C (ONLY THE A RESIDUES), 10 REMARK 210 MM PHOSPHATE BUFFER (PH 6.8), REMARK 210 10 MM KCL, 0.02 MM EDTA, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D_13C-SEPARATED_ REMARK 210 NOESY, 15N, AND 13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000 REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR REMARK 210 DYNAMICS, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 18 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : AVERAGED STRUCTURE 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 O2' G A 1 O4' G A 2 1.58 REMARK 500 O2' G A 8 O2' U A 9 1.91 REMARK 500 O2' G A 1 C5' G A 2 1.96 REMARK 500 O2' A A 26 C5' C A 27 2.02 REMARK 500 O2' G A 32 O4' C A 33 2.05 REMARK 500 O2' G A 1 C4' G A 2 2.06 REMARK 500 O2' G A 8 O4' U A 9 2.06 REMARK 500 O2' G A 28 N7 G A 29 2.19 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 U A 9 C4' - C3' - O3' ANGL. DEV. = -18.3 DEGREES REMARK 500 U A 9 C4' - C3' - C2' ANGL. DEV. = -68.5 DEGREES REMARK 500 U A 9 C3' - C2' - C1' ANGL. DEV. = 9.0 DEGREES REMARK 500 U A 9 O4' - C1' - C2' ANGL. DEV. = -66.9 DEGREES REMARK 500 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 A A 12 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 A A 14 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 A A 15 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 A A 16 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 A A 17 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 A A 20 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 A A 21 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 A A 22 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 C A 23 C2' - C3' - O3' ANGL. DEV. = -17.3 DEGREES REMARK 500 A A 24 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 25 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 G A 25 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 25 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 A A 26 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 G A 28 C4' - C3' - C2' ANGL. DEV. = -13.4 DEGREES REMARK 500 G A 28 C3' - C2' - C1' ANGL. DEV. = 7.5 DEGREES REMARK 500 G A 28 O4' - C1' - C2' ANGL. DEV. = -12.5 DEGREES REMARK 500 G A 28 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 G A 28 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 G A 28 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 29 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 G A 29 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 G A 31 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 G A 32 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 C A 33 C4' - C3' - O3' ANGL. DEV. = -19.3 DEGREES REMARK 500 C A 33 C4' - C3' - C2' ANGL. DEV. = -71.5 DEGREES REMARK 500 C A 33 C3' - C2' - C1' ANGL. DEV. = 10.9 DEGREES REMARK 500 C A 33 O4' - C1' - C2' ANGL. DEV. = -64.5 DEGREES REMARK 500 C A 33 N1 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 C A 33 O4' - C1' - N1 ANGL. DEV. = -8.1 DEGREES REMARK 500 C A 34 C3' - C2' - C1' ANGL. DEV. = 6.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G A 25 0.05 SIDE_CHAIN REMARK 500 G A 29 0.05 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6115 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFTS DBREF 1T28 A 1 34 PDB 1T28 1T28 1 34 SEQRES 1 A 34 G G U C A U C G U U G A G SEQRES 2 A 34 A A A A C G A A A C A G A SEQRES 3 A 34 C G G U G G 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 MASTER 160 0 0 0 0 0 0 6 0 0 0 3 END