HEADER RNA 20-OCT-09 2KPV TITLE NMR MODEL OF THE FIRST LET-7 MIRNA COMPLEMENTARY SITE (LCS1) IN 3'-UTR TITLE 2 OF LIN-41 MRNA FROM C. ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (34-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION USING T7 SOURCE 4 RNA POLYMERASE AND DNA OLIGONUCLEOTIDE TEMPLATE KEYWDS STEM-LOOP, ADENINE BULGE, ASYMMETRIC INTERNAL LOOP, RESIDUAL DIPOLAR KEYWDS 2 COUPLINGS, GAAA TETRALOOP, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.CEVEC,C.THIBAUDEAU,J.PLAVEC REVDAT 2 07-SEP-11 2KPV 1 JRNL VERSN REVDAT 1 04-AUG-10 2KPV 0 JRNL AUTH M.CEVEC,C.THIBAUDEAU,J.PLAVEC JRNL TITL NMR STRUCTURE OF THE LET-7 MIRNA INTERACTING WITH THE SITE JRNL TITL 2 LCS1 OF LIN-41 MRNA FROM CAENORHABDITIS ELEGANS. JRNL REF NUCLEIC ACIDS RES. V. 38 7814 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 20660479 JRNL DOI 10.1093/NAR/GKQ640 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 810 NOE-DERIVED DISTANCE RESTRAINTS, REMARK 3 138 TORSION ANGLE RESTRAINTS, 52 RESIDUAL DIPOLAR COUPLING REMARK 3 RESTRAINTS, 32 HYDROGEN BOND RESTRAINTS AND 24 PLANARITY REMARK 3 RESTRAINTS. REMARK 4 REMARK 4 2KPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB101424. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 278 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 20; 20 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM [U-100% 13C; U-100% 15N] RNA REMARK 210 (34-MER)-1, 10MM SODIUM PHOSPHATE REMARK 210 -2, 20MM SODIUM CHLORIDE-3, 95% REMARK 210 H2O/5% D2O; 2MM [U-100% 13C; U- REMARK 210 100% 15N] RNA (34-MER)-4, 10MM REMARK 210 SODIUM PHOSPHATE-5, 20MM SODIUM REMARK 210 CHLORIDE-6, 100% D2O; 1MM [U-100% REMARK 210 13C; U-100% 15N] RNA (34-MER)-7, REMARK 210 10MM SODIUM PHOSPHATE-8, 20MM REMARK 210 SODIUM CHLORIDE-9, 17MG/ML PF1 REMARK 210 PHAGE-10, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D 15N-HSQC; 2D 13C- REMARK 210 HSQC; 2D DQF-COSY; 2D HNN-COSY; REMARK 210 2D TOCSY; 2D 1H-31P COSY; 2D 15N- REMARK 210 IPAP-HSQC; 3D HCCH-TOCSY; 3D HCCH REMARK 210 -COSY; 3D 13C-SEPARATED-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2002, VNMRJ 2.1B REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY AND LEAST RESTRAINT REMARK 210 VIOLATIONS 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: 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: 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 A A 30 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 34 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 2 C A 29 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 2 C A 34 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 3 A A 30 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 C A 34 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 4 C A 29 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 4 C A 34 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 5 C A 34 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 6 A A 30 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 C A 34 C3' - C2' - C1' ANGL. DEV. = 5.1 DEGREES REMARK 500 7 A A 30 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 C A 34 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 8 C A 34 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 9 C A 34 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 10 A A 30 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 C A 34 C3' - C2' - C1' ANGL. DEV. = 5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2KPV A 1 34 PDB 2KPV 2KPV 1 34 SEQRES 1 A 34 G G A G G U A G U A G G U SEQRES 2 A 34 C G A A A G A C C G U U C SEQRES 3 A 34 U A C A C U 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 119 0 0 0 0 0 0 6 0 0 0 3 END