HEADER RNA 06-OCT-03 1R4H TITLE NMR SOLUTION STRUCTURE OF THE IIIC DOMAIN OF GB VIRUS B IRES ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*GP*CP*AP*AP*GP*CP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE OCCURS NATURALLY IN GB VIRUS B AND WAS SOURCE 4 SYNTHESIZED IN VITRO TRANCRIPTION USING T7 RNA POLYMERASE. KEYWDS GB VIRUS B, IRES, HAIRPIN LOOP, RNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR K.KALUARACHCHI,V.THIVIYANATHAN,R.RIJINBRAND,S.M.LEMON,D.G.GORENSTEIN REVDAT 4 02-MAR-22 1R4H 1 REMARK REVDAT 3 24-FEB-09 1R4H 1 VERSN REVDAT 2 15-FEB-05 1R4H 1 JRNL REVDAT 1 19-OCT-04 1R4H 0 JRNL AUTH R.RIJNBRAND,V.THIVIYANATHAN,K.KALUARACHCHI,S.M.LEMON, JRNL AUTH 2 D.G.GORENSTEIN JRNL TITL MUTATIONAL AND STRUCTURAL ANALYSIS OF STEM-LOOP IIIC OF THE JRNL TITL 2 HEPATITIS C VIRUS AND GB VIRUS B INTERNAL RIBOSOME ENTRY JRNL TITL 3 SITES. JRNL REF J.MOL.BIOL. V. 343 805 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15476802 JRNL DOI 10.1016/J.JMB.2004.08.095 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER, A REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R4H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020425. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 10 MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10 MM PHOSPHATE, 10 MM KCL, 0.05 REMARK 210 MM EDTA PH 6.8, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING RESTRAINED MOLECULAR REMARK 210 DYNAMICS COMPLETE RELAXATION REMARK 210 MATRIX REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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: 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 H1' A A 5 H5' A A 6 1.12 REMARK 500 H41 C A 4 O6 G A 7 1.40 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. = 4.4 DEGREES REMARK 500 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1R4H A 1 10 PDB 1R4H 1R4H 1 10 SEQRES 1 A 10 G G G C A A G C 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