10 20 30 40 50 60 70 80 2F87 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 02-DEC-05 2F87
TITLE SOLUTION STRUCTURE OF A GAAG TETRALOOP IN SRP RNA FROM TITLE 2 PYROCOCCUS FURIOSUS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SRP RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PFHE6-12; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE RNA FRAGMENT, PFHE6-12 WAS CHEMICALLY SOURCE 4 SYNTHESIZED BY A PHOSPHORAMIDITE METHOD, USING AN SOURCE 5 AUTOMATIC DNA/RNA SYNTHESIZER, EXPEDITE MODEL 8909 SOURCE 6 (PERSEPTIVE BIOSYSTEMS).
KEYWDS SRP, GNRR, RNA
EXPDTA SOLUTION NMR
NUMMDL 13
MDLTYP MINIMIZED AVERAGE
AUTHOR K.OKADA,M.TAKAHASHI,T.SAKAMOTO,K.NAKAMURA,A.KANAI,G KAWAI
REVDAT 2 24-FEB-09 2F87 1 VERSN REVDAT 1 08-AUG-06 2F87 0
JRNL AUTH K.OKADA,M.TAKAHASHI,T.SAKAMOTO,G.KAWAI,K.NAKAMURA, JRNL AUTH 2 A.KANAI JRNL TITL SOLUTION STRUCTURE OF A GAAG TETRALOOP IN HELIX 6 JRNL TITL 2 OF SRP RNA FROM PYROCOCCUS FURIOSUS JRNL REF NUCLEOSIDES NUCLEOTIDES V. 25 383 2006 JRNL REF 2 NUCLEIC ACIDS JRNL REFN ISSN 1525-7770 JRNL PMID 16838833 JRNL DOI 10.1080/15257770600683979
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 3 179 RESTRAINTS, 127 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 34 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 18 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS.
REMARK 4 REMARK 4 2F87 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-DEC-05. REMARK 100 THE RCSB ID CODE IS RCSB035572.
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 : 50MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0MM RNA BUFFER NA; 95% H2O, REMARK 210 5% D2O; 2.0MM RNA; 20MM REMARK 210 PHOSPHATE BUFFER NA; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY 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 : DISCOVER 97.0, XWINNMR 2.6, REMARK 210 FELIX 97.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 13 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR 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 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 G A 2 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 C A 3 O4' - C1' - N1 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 C A 12 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 2 C A 3 O4' - C1' - N1 ANGL. DEV. = 7.9 DEGREES REMARK 500 2 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 C A 12 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 3 G A 2 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 3 C A 3 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 U A 4 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 3 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 4 G A 2 O4' - C1' - N9 ANGL. DEV. = 8.1 DEGREES REMARK 500 4 C A 3 O4' - C1' - N1 ANGL. DEV. = 7.9 DEGREES REMARK 500 4 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 C A 12 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 5 G A 2 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 5 C A 3 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 5 U A 4 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 5 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 C A 12 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 6 G A 2 O4' - C1' - N9 ANGL. DEV. = 8.1 DEGREES REMARK 500 6 C A 3 O4' - C1' - N1 ANGL. DEV. = 8.1 DEGREES REMARK 500 6 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 7 G A 2 O4' - C1' - N9 ANGL. DEV. = 7.8 DEGREES REMARK 500 7 C A 3 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 7 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 C A 12 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 8 G A 1 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 8 G A 2 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 8 C A 3 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 8 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 8 A A 7 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 C A 11 C5' - C4' - O4' ANGL. DEV. = 5.6 DEGREES REMARK 500 8 C A 12 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 9 G A 1 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 9 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 9 G A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 C A 3 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 9 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 10 G A 2 O4' - C1' - N9 ANGL. DEV. = 8.4 DEGREES REMARK 500 10 C A 3 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 10 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 68 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 G A 1 0.05 SIDE_CHAIN REMARK 500 1 G A 2 0.07 SIDE_CHAIN REMARK 500 1 G A 5 0.06 SIDE_CHAIN REMARK 500 1 C A 12 0.07 SIDE_CHAIN REMARK 500 2 G A 1 0.05 SIDE_CHAIN REMARK 500 2 G A 2 0.07 SIDE_CHAIN REMARK 500 2 G A 5 0.07 SIDE_CHAIN REMARK 500 2 C A 12 0.08 SIDE_CHAIN REMARK 500 3 G A 2 0.06 SIDE_CHAIN REMARK 500 3 C A 3 0.08 SIDE_CHAIN REMARK 500 3 U A 4 0.09 SIDE_CHAIN REMARK 500 3 G A 5 0.07 SIDE_CHAIN REMARK 500 3 G A 10 0.07 SIDE_CHAIN REMARK 500 3 C A 12 0.07 SIDE_CHAIN REMARK 500 4 G A 1 0.05 SIDE_CHAIN REMARK 500 4 G A 2 0.07 SIDE_CHAIN REMARK 500 4 A A 6 0.06 SIDE_CHAIN REMARK 500 4 G A 8 0.06 SIDE_CHAIN REMARK 500 4 G A 9 0.07 SIDE_CHAIN REMARK 500 4 C A 12 0.08 SIDE_CHAIN REMARK 500 5 G A 2 0.07 SIDE_CHAIN REMARK 500 5 C A 3 0.07 SIDE_CHAIN REMARK 500 5 G A 9 0.07 SIDE_CHAIN REMARK 500 5 C A 12 0.08 SIDE_CHAIN REMARK 500 6 G A 1 0.05 SIDE_CHAIN REMARK 500 6 G A 2 0.07 SIDE_CHAIN REMARK 500 6 G A 5 0.06 SIDE_CHAIN REMARK 500 6 C A 12 0.08 SIDE_CHAIN REMARK 500 7 G A 2 0.07 SIDE_CHAIN REMARK 500 7 C A 3 0.09 SIDE_CHAIN REMARK 500 7 G A 9 0.05 SIDE_CHAIN REMARK 500 7 C A 12 0.07 SIDE_CHAIN REMARK 500 8 C A 3 0.08 SIDE_CHAIN REMARK 500 8 U A 4 0.06 SIDE_CHAIN REMARK 500 8 G A 5 0.07 SIDE_CHAIN REMARK 500 8 C A 11 0.06 SIDE_CHAIN REMARK 500 9 C A 3 0.07 SIDE_CHAIN REMARK 500 9 G A 5 0.07 SIDE_CHAIN REMARK 500 9 C A 12 0.14 SIDE_CHAIN REMARK 500 10 G A 2 0.07 SIDE_CHAIN REMARK 500 10 C A 3 0.10 SIDE_CHAIN REMARK 500 10 G A 5 0.05 SIDE_CHAIN REMARK 500 10 A A 6 0.06 SIDE_CHAIN REMARK 500 10 G A 8 0.05 SIDE_CHAIN REMARK 500 11 G A 1 0.05 SIDE_CHAIN REMARK 500 11 G A 2 0.07 SIDE_CHAIN REMARK 500 11 C A 3 0.06 SIDE_CHAIN REMARK 500 11 G A 5 0.06 SIDE_CHAIN REMARK 500 11 A A 6 0.05 SIDE_CHAIN REMARK 500 11 C A 12 0.08 SIDE_CHAIN REMARK 500 12 G A 2 0.06 SIDE_CHAIN REMARK 500 12 G A 9 0.06 SIDE_CHAIN REMARK 500 12 C A 12 0.07 SIDE_CHAIN REMARK 500 13 G A 2 0.08 SIDE_CHAIN REMARK 500 13 C A 3 0.06 SIDE_CHAIN REMARK 500 13 U A 4 0.08 SIDE_CHAIN REMARK 500 13 G A 9 0.07 SIDE_CHAIN REMARK 500 13 G A 10 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 2F87 A 1 12 PDB 2F87 2F87 1 12
SEQRES 1 A 12 G G C U G A A G G 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