PDB Short entry for 1XV6 HEADER RNA 27-OCT-04 1XV6 TITLE THE SOLUTION STRUCTURE OF 2',5'-LINKED 3'-O-(2-METHOXYETHYL)-RNA TITLE 2 HAIRPIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*(C2L)P*(G2L)P*(C2L)P*(G2L)P*(A2L)P*(A2L)P*(U2L) COMPND 3 P*(U2L)P*(C2L)P*(G2L)P*(C2L)P*(G2L))-2'; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: 2'-MOE RNA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE CHEMISTRY KEYWDS HAIRPIN, (2', 5')-RNA, 3'-O-(2-METHOXYETHYL) RIBOSE, RNA EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR M.PLEVNIK,Z.GDANIEC,J.PLAVEC REVDAT 3 02-MAR-22 1XV6 1 REMARK LINK REVDAT 2 24-FEB-09 1XV6 1 VERSN REVDAT 1 05-APR-05 1XV6 0 JRNL AUTH M.PLEVNIK,Z.GDANIEC,J.PLAVEC JRNL TITL SOLUTION STRUCTURE OF A MODIFIED 2',5'-LINKED RNA HAIRPIN JRNL TITL 2 INVOLVED IN AN EQUILIBRIUM WITH DUPLEX JRNL REF NUCLEIC ACIDS RES. V. 33 1749 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 15788747 JRNL DOI 10.1093/NAR/GKI318 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, AMBER 6 REMARK 3 AUTHORS : VARIAN (VNMR), KOLLMAN ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES WERE REFINED BY NMR RESTRAINED MOLECULAR DYNAMICS IN REMARK 3 TWO STAGES USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. REMARK 3 THE RESULTING STRUCTURES WERE SUBJECTED TO ENERGY MINIMIZATION. REMARK 3 2',5' PHOSPHODIESTER LINKAGES BETWEEN RESIDUES, O3* OF EACH RIBOSE REMARK 3 MODIFIED BY METHOXYETHYL. REMARK 4 REMARK 4 1XV6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030800. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 50MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9MM HAIRPIN, 100% D2O, 50MM REMARK 210 NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000 REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 18 REMARK 210 REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND REMARK 210 HETERONUCLEAR 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 DBREF 1XV6 A 1 12 PDB 1XV6 1XV6 1 12 SEQRES 1 A 12 C2L G2L C2L G2L A2L A2L U2L U2L C2L G2L C2L G2L MODRES 1XV6 C2L A 1 C MODRES 1XV6 G2L A 2 G MODRES 1XV6 C2L A 3 C MODRES 1XV6 G2L A 4 G MODRES 1XV6 A2L A 5 A MODRES 1XV6 A2L A 6 A MODRES 1XV6 U2L A 7 U MODRES 1XV6 U2L A 8 U MODRES 1XV6 C2L A 9 C MODRES 1XV6 G2L A 10 G MODRES 1XV6 C2L A 11 C MODRES 1XV6 G2L A 12 G HET C2L A 1 42 HET G2L A 2 44 HET C2L A 3 44 HET G2L A 4 44 HET A2L A 5 43 HET A2L A 6 43 HET U2L A 7 43 HET U2L A 8 43 HET C2L A 9 44 HET G2L A 10 44 HET C2L A 11 44 HET G2L A 12 45 HETNAM C2L 5-METHYL-3'-O-METHOXYETHYL CYTIDINE 5'-MONOPHOSPHATE HETNAM G2L 3'-O-METHYOXYETHYL-GUANOSINE-5'-MONOPHOSPHATE HETNAM A2L 3'-O-METHYOXYETHYL-ADENOSINE 5'-MONOPHOSPHATE HETNAM U2L 5-METHYL-3'-O-METHOXYETHYL URIDINE-5'-MONOPHOSPHATE FORMUL 1 C2L 4(C13 H22 N3 O9 P) FORMUL 1 G2L 4(C13 H20 N5 O9 P) FORMUL 1 A2L 2(C13 H20 N5 O8 P) FORMUL 1 U2L 2(C13 H21 N2 O10 P) LINK O2' C2L A 1 P G2L A 2 1555 1555 1.63 LINK O2' G2L A 2 P C2L A 3 1555 1555 1.60 LINK O2' C2L A 3 P G2L A 4 1555 1555 1.62 LINK O2' G2L A 4 P A2L A 5 1555 1555 1.63 LINK O2' A2L A 5 P A2L A 6 1555 1555 1.61 LINK O2' A2L A 6 P U2L A 7 1555 1555 1.62 LINK O2' U2L A 7 P U2L A 8 1555 1555 1.65 LINK O2' U2L A 8 P C2L A 9 1555 1555 1.62 LINK O2' C2L A 9 P G2L A 10 1555 1555 1.61 LINK O2' G2L A 10 P C2L A 11 1555 1555 1.61 LINK O2' C2L A 11 P G2L A 12 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