HEADER RNA 13-JUL-12 2LVY TITLE SOLUTION STRUCTURE OF A RNA DUPLEX CONTAINING A 2'-O-PIVALOYLOXYMETHYL TITLE 2 MODIFICATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(*GP*CP*GP*UP*AP*GP*CP*GP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS RNA, MODIFICATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.BARAGUEY REVDAT 2 01-MAY-24 2LVY 1 REMARK LINK REVDAT 1 10-APR-13 2LVY 0 JRNL AUTH C.BARAGUEY,E.LESCRINIER,T.LAVERGNE,F.DEBART,P.HERDEWIJN, JRNL AUTH 2 J.J.VASSEUR JRNL TITL THE BIOLABILE 2'-O-PIVALOYLOXYMETHYL MODIFICATION IN AN RNA JRNL TITL 2 HELIX: AN NMR SOLUTION STRUCTURE. JRNL REF ORG.BIOMOL.CHEM. V. 11 2638 2013 JRNL REFN ISSN 1477-0520 JRNL PMID 23455628 JRNL DOI 10.1039/C3OB27005J REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.25, X-PLOR NIH 2.25 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LVY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000102899. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 283 REMARK 210 PH : 6.7; 6.7 REMARK 210 IONIC STRENGTH : 0; 0 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9 MM DUPLEX, 100% D2O; 0.9 MM REMARK 210 DUPLEX, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-31P HETCOR; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 7 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 7 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 8 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 8 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 8 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 9 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 9 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 10 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 10 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 11 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 11 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 11 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 12 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 12 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 13 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 13 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 14 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 14 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 14 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 15 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 15 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 15 DT B 18 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 15 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 16 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 16 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 16 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 16 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 17 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 17 DT B 18 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 17 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 18 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 56 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18593 RELATED DB: BMRB DBREF 2LVY A 1 9 PDB 2LVY 2LVY 1 9 DBREF 2LVY B 10 18 PDB 2LVY 2LVY 10 18 SEQRES 1 A 9 C G C UPV A C G C DT SEQRES 1 B 9 G C G U A G C G DT MODRES 2LVY UPV A 4 U HET UPV A 4 48 HETNAM UPV 2'-O-{[(2,2-DIMETHYLPROPANOYL)OXY]METHYL}URIDINE 5'- HETNAM 2 UPV (DIHYDROGEN PHOSPHATE) FORMUL 1 UPV C15 H23 N2 O11 P LINK O3' C A 3 P UPV A 4 1555 1555 1.61 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