HEADER RNA 04-JUN-04 1WKS TITLE SOLUTION STRUCTURE OF AN RNA STEM-LOOP DERIVED FROM THE 3' CONSERVED TITLE 2 REGION OF EEL LINE UNAL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*UP*UP*UP*GP*GP*AP*UP*AP*AP*AP*AP*GP*CP*C)- COMPND 3 3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICAL SYNTHESIZED 17-MER RNA CORRESPONDING TO THE SOURCE 4 RT BINDING SITE OF EEL LINE RNA. KEYWDS RNA, PENTALOOP, LINE, RETROTRANSPOSITION EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR S.BABA,M.KAJIKAWA,N.OKADA,G.KAWAI REVDAT 4 02-MAR-22 1WKS 1 REMARK REVDAT 3 24-FEB-09 1WKS 1 VERSN REVDAT 2 21-SEP-04 1WKS 1 JRNL REVDAT 1 22-JUN-04 1WKS 0 JRNL AUTH S.BABA,M.KAJIKAWA,N.OKADA,G.KAWAI JRNL TITL SOLUTION STRUCTURE OF AN RNA STEM-LOOP DERIVED FROM THE 3' JRNL TITL 2 CONSERVED REGION OF EEL LINE UNAL2 JRNL REF RNA V. 10 1380 2004 JRNL REFN ISSN 1355-8382 JRNL PMID 15273327 JRNL DOI 10.1261/RNA.7460104 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, DISCOVER 97.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), ACCELRYS (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 298 RESTRAINTS, 204 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 80 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 14 DISTANCE RESTRAINTS FROM HYDROGEN REMARK 3 BONDS. REMARK 4 REMARK 4 1WKS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023685. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM RNA FRAGMENT; 10MM PHOSPHATE REMARK 210 BUFFER, 50 MM NACL; 100% D2O; REMARK 210 1MM RNA FRAGMENT; 10MM PHOSPHATE REMARK 210 BUFFER, 50 MM NACL; 90% H2O, 10% REMARK 210 D2O; 1MM RNA FRAGMENT (15N, 13C- REMARK 210 GUANOSINE, URIDINE LABELED 36- REMARK 210 MER RNA); 10MM PHOSPHATE BUFFER, REMARK 210 50 MM NACL; 100% D2O; 1MM RNA REMARK 210 FRAGMENT (15N, 13C-GUANOSINE, REMARK 210 URIDINE LABELED 36-MER RNA); REMARK 210 10MM PHOSPHATE BUFFER, 50 MM REMARK 210 NACL; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; 2D REMARK 210 -HSQC; 1D-HSQC-SELECTED SPECTRUM; REMARK 210 1D-HSQC-FILTERED SPECTRUM REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97.0, DISCOVER 97.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 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: 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 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 G A 8 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 15 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 U A 5 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 8 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 3 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 15 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 4 G A 8 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 G A 8 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 6 A A 11 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 6 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 7 G A 8 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 7 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 8 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 153 ANGLE DEVIATIONS. 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 1 A A 11 0.07 SIDE CHAIN REMARK 500 2 U A 4 0.07 SIDE CHAIN REMARK 500 2 A A 12 0.06 SIDE CHAIN REMARK 500 3 U A 5 0.07 SIDE CHAIN REMARK 500 4 G A 1 0.07 SIDE CHAIN REMARK 500 4 U A 4 0.07 SIDE CHAIN REMARK 500 4 A A 12 0.11 SIDE CHAIN REMARK 500 4 G A 15 0.07 SIDE CHAIN REMARK 500 5 A A 11 0.06 SIDE CHAIN REMARK 500 5 A A 12 0.07 SIDE CHAIN REMARK 500 5 G A 15 0.07 SIDE CHAIN REMARK 500 6 U A 4 0.06 SIDE CHAIN REMARK 500 6 G A 15 0.08 SIDE CHAIN REMARK 500 7 U A 4 0.08 SIDE CHAIN REMARK 500 7 A A 11 0.07 SIDE CHAIN REMARK 500 8 U A 4 0.07 SIDE CHAIN REMARK 500 9 A A 12 0.06 SIDE CHAIN REMARK 500 11 U A 4 0.06 SIDE CHAIN REMARK 500 11 A A 11 0.07 SIDE CHAIN REMARK 500 11 G A 15 0.08 SIDE CHAIN REMARK 500 12 U A 4 0.07 SIDE CHAIN REMARK 500 13 U A 4 0.07 SIDE CHAIN REMARK 500 14 A A 12 0.08 SIDE CHAIN REMARK 500 15 U A 4 0.07 SIDE CHAIN REMARK 500 16 A A 12 0.05 SIDE CHAIN REMARK 500 17 A A 11 0.09 SIDE CHAIN REMARK 500 17 A A 12 0.07 SIDE CHAIN REMARK 500 18 U A 4 0.06 SIDE CHAIN REMARK 500 18 A A 12 0.05 SIDE CHAIN REMARK 500 19 U A 4 0.06 SIDE CHAIN REMARK 500 20 U A 6 0.07 SIDE CHAIN REMARK 500 21 A A 11 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1WKS A 1 17 PDB 1WKS 1WKS 1 17 SEQRES 1 A 17 G G C U U U G G A U A A A SEQRES 2 A 17 A 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 MODEL 1