10 20 30 40 50 60 70 80 1WKS - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 04-JUN-04 1WKS
TITLE SOLUTION STRUCTURE OF AN RNA STEM-LOOP DERIVED FROM THE 3' TITLE 2 CONSERVED REGION OF EEL LINE UNAL2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*GP*GP*CP*UP*UP*UP*GP*GP*AP*UP*AP*AP*AP*AP*GP*CP*C)-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 SOURCE 4 CORRESPONDING TO THE RT BINDING SITE OF EEL LINE RNA.
KEYWDS NMR, RNA, PENTALOOP, LINE, RETROTRANSPOSITION
EXPDTA SOLUTION NMR
NUMMDL 21
MDLTYP MINIMIZED AVERAGE
AUTHOR S.BABA,M.KAJIKAWA,N.OKADA,G.KAWAI
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 JRNL TITL 2 FROM THE 3' 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 97.0 REMARK 3 AUTHORS : ACCELRYS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 298 RESTRAINTS, 204 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 80 DIHEDRAL ANGLE RESTRAINTS, 14 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN 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 RCSB ID CODE IS RCSB023685.
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 REMARK 210 PHOSPHATE BUFFER, 50 MM NACL; REMARK 210 100% D2O; 1MM RNA FRAGMENT; REMARK 210 10MM PHOSPHATE BUFFER, 50 MM REMARK 210 NACL; 90% H2O, 10% D2O; 1MM REMARK 210 RNA FRAGMENT (15N, 13C- REMARK 210 GUANOSINE, URIDINE LABELED 36- REMARK 210 MER RNA); 10MM PHOSPHATE REMARK 210 BUFFER, 50 MM NACL; 100% D2O; REMARK 210 1MM RNA FRAGMENT (15N, 13C- REMARK 210 GUANOSINE, URIDINE LABELED 36- REMARK 210 MER RNA); 10MM PHOSPHATE REMARK 210 BUFFER, 50 MM NACL; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY, REMARK 210 2D-HSQC, 1D-HSQC-SELECTED REMARK 210 SPECTRUM, 1D-HSQC-FILTERED REMARK 210 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 : XWINNMR 2.6, FELIX 97.0, REMARK 210 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 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. = 5.1 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. = 5.1 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. = 4.4 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