10 20 30 40 50 60 70 80 1XWU - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 02-NOV-04 1XWU
TITLE SOLUTION STRUCTURE OF ACAUAGA LOOP
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*CP*GP*AP*AP*AP*CP*AP*UP*AP*GP*AP*UP*UP*CP*GP*A)-3'; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: ACAUAGA HEPTA-NUCLEOTIDE LOOP; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS HAIRPIN LOOP, RNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR T.SAKAMOTO,A.OGURO,G.KAWAI,T.OHTSU,Y.NAKAMURA
REVDAT 2 24-FEB-09 1XWU 1 VERSN REVDAT 1 15-FEB-05 1XWU 0
JRNL AUTH T.SAKAMOTO,A.OGURO,G.KAWAI,T.OHTSU,Y.NAKAMURA JRNL TITL NMR STRUCTURES OF DOUBLE LOOPS OF AN RNA APTAMER JRNL TITL 2 AGAINST MAMMALIAN INITIATION FACTOR 4A JRNL REF NUCLEIC ACIDS RES. V. 33 745 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 15687383 JRNL DOI 10.1093/NAR/GKI222
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 97.0 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 292 RESTRAINTS, 228 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 46 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 13 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS, 5 BASE PLANARITY RESTRAINTS.
REMARK 4 REMARK 4 1XWU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-04. REMARK 100 THE RCSB ID CODE IS RCSB030858.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 70 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM RNA; 20MM PHOSPHATE REMARK 210 BUFFER NA, 50MM NACL; 95% H2O, REMARK 210 5% D2O; 0.5MM RNA; 20MM REMARK 210 PHOSPHATE BUFFER NA, 50MM REMARK 210 NACL; 100% D2O; 1MM RNA U-15N, REMARK 210 13C; 20MM PHOSPHATE BUFFER NA, REMARK 210 50MM NACL; 95% H2O, 5% D2O; REMARK 210 1MM RNA U-15N,13C; 20MM REMARK 210 PHOSPHATE BUFFER NA, 50MM REMARK 210 NACL; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY, REMARK 210 HP-COSY, HCP 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 : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY.
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 C A 1 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 A A 9 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 U A 12 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 G A 15 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES 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 A A 5 0.05 SIDE_CHAIN REMARK 500 A A 9 0.06 SIDE_CHAIN REMARK 500 U A 12 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XWP RELATED DB: PDB REMARK 900 ANOTHER HAIRPIN LOOP DOMAIN OF AN RNA APTAMER AGAINST REMARK 900 MAMMALIAN INITIATION FACTOR 4A
DBREF 1XWU A 1 16 PDB 1XWU 1XWU 1 16
SEQRES 1 A 16 C G A A A C A U A G A U U SEQRES 2 A 16 C G A
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