1K8S - Header Asymmetric Unit

HEADER RNA 25-OCT-01 1K8S

TITLE BULGED ADENOSINE IN AN RNA DUPLEX

COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*AP*GP*AP*GP*UP*GP*CP*CP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: BULGED BASE RNA DUPLEX E COLI 5S RRNA; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*GP*CP*GP*GP*CP*AP*CP*CP*UP*GP*CP*C)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: ENZYMATICALLY SYNTHESIZED USING T7 RNA SOURCE 4 POLYMERASE.; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: ENZYMATICALLY SYNTHESIZED USING T7 RNA SOURCE 8 POLYMERASE.

KEYWDS BULGED BASE, BULGED ADENOSINE, BULGED RNA, RNA BULGES

EXPDTA SOLUTION NMR

AUTHOR V.THIVIYANATHAN,A.B.GULIAEV,N.B.LEONTIS,D.G.GORENSTEIN

REVDAT 2 24-FEB-09 1K8S 1 VERSN REVDAT 1 14-NOV-01 1K8S 0

JRNL AUTH V.THIVIYANATHAN,A.B.GULIAEV,N.B.LEONTIS, JRNL AUTH 2 D.G.GORENSTEIN JRNL TITL SOLUTION CONFORMATION OF A BULGED ADENOSINE BASE JRNL TITL 2 IN AN RNA DUPLEX BY RELAXATION MATRIX REFINEMENT. JRNL REF J.MOL.BIOL. V. 300 1143 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10903860 JRNL DOI 10.1006/JMBI.2000.3931

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : UCSF REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1K8S COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-01. REMARK 100 THE RCSB ID CODE IS RCSB014702.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 110 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 MM NACL, 10 MM SODIUM REMARK 210 PHOSPHATE, 0.02 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : VXRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95, MORASS 2.1 REMARK 210 METHOD USED : MATRIX RELAXATION, MOLECULAR REMARK 210 DYNAMICS, TORSION ANGLE REMARK 210 DYNAMICS 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: 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 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 A A 4 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 A A 6 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 6 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 U A 8 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 C A 11 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 C A 11 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 G A 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 C A 13 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 C B 15 C3' - C2' - C1' ANGL. DEV. = 5.9 DEGREES REMARK 500 C B 15 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 G B 16 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 C B 18 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 A B 19 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 A B 19 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 C B 20 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 C B 21 C3' - C2' - C1' ANGL. DEV. = 5.1 DEGREES REMARK 500 U B 22 C3' - C2' - C1' ANGL. DEV. = 5.3 DEGREES REMARK 500 U B 22 O4' - C1' - N1 ANGL. DEV. = 5.1 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 4 0.07 SIDE_CHAIN REMARK 500 G A 7 0.05 SIDE_CHAIN REMARK 500 G A 9 0.09 SIDE_CHAIN REMARK 500 C A 11 0.09 SIDE_CHAIN REMARK 500 G A 12 0.08 SIDE_CHAIN REMARK 500 C A 13 0.09 SIDE_CHAIN REMARK 500 C B 20 0.06 SIDE_CHAIN REMARK 500 C B 21 0.10 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL

DBREF 1K8S A 1 13 PDB 1K8S 1K8S 1 13 DBREF 1K8S B 14 25 PDB 1K8S 1K8S 14 25

SEQRES 1 A 13 G G C A G A G U G C C G C SEQRES 1 B 12 G C G G C A C C U 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