229D - Header Asymmetric Unit

HEADER DNA 16-AUG-95 229D

TITLE DNA ANALOG OF YEAST TRANSFER RNA PHE ANTICODON DOMAIN WITH TITLE 2 MODIFIED BASES 5-METHYL CYTOSINE AND 1-METHYL GUANINE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*AP*GP*AP*CP*(UMP) COMPND 3 P*GP*AP*AP*(MG1)P*AP*(UMP)P*(5CM)P*(UMP)P*GP*G)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED

KEYWDS DNA, TRANSFER RNA, ANTICODON, HAIRPIN LOOP

EXPDTA SOLUTION NMR

AUTHOR M.M.BASTI,J.W.STUART,A.T.LAM,R.GUENTHER,P.F.AGRIS

REVDAT 2 24-FEB-09 229D 1 VERSN REVDAT 1 07-DEC-95 229D 0

JRNL AUTH M.M.BASTI,J.W.STUART,A.T.LAM,R.GUENTHER,P.F.AGRIS JRNL TITL DESIGN, BIOLOGICAL ACTIVITY AND NMR-SOLUTION JRNL TITL 2 STRUCTURE OF A DNA ANALOGUE OF YEAST TRNA(PHE) JRNL TITL 3 ANTICODON DOMAIN. JRNL REF NAT.STRUCT.BIOL. V. 3 38 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8548453 JRNL DOI 10.1038/NSB0196-38

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.H.MOORE,L.VAN MEERVELT,S.A.SALISBURY,P.K.T.LIN, REMARK 1 AUTH 2 D.M.BROWN REMARK 1 TITL DIRECT OBSERVATION OF TWO BASE-PAIRING MODES OF A REMARK 1 TITL 2 CYTOSINE-THYMINE ANALOGUE WITH GUANINE IN A DNA REMARK 1 TITL 3 Z-FORM DUPLEX: SIGNIFICANCE FOR BASE ANALOGUE REMARK 1 TITL 4 MUTAGENESIS REMARK 1 REF J.MOL.BIOL. V. 251 665 1995 REMARK 1 REFN ISSN 0022-2836

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : BIOSYM TECHNOLOGIES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NUMBER OF ATOMS USED IN REFINEMENT. REMARK 3 NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 537 REMARK 3 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE REMARK 3 SOLUTION STRUCTURE OF THE 17-MER DNA HAIRPIN LOOP WAS REMARK 3 DETERMINED BASED ON 246 DISTANCE AND DIHEDRAL RESTRAINTS REMARK 3 ESTIMATED FROM 2D NOE SPECTRUM. TEN LOW ENERGY STRUCTURES WERE REMARK 3 USED TO GENERATE THIS AVERAGE STRUCTURE WHICH WAS FURTHER REMARK 3 ENERGY MINIMIZED.

REMARK 4 REMARK 4 229D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL 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 DC A 2 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 19.9 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG A 8 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 9 O4' - C1' - C2' ANGL. DEV. = 4.5 DEGREES REMARK 500 DA A 9 N9 - C1' - C2' ANGL. DEV. = 25.2 DEGREES REMARK 500 DA A 9 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 12 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 16 O4' - C1' - N9 ANGL. DEV. = 7.3 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 DC A 2 0.12 SIDE_CHAIN REMARK 500 DA A 3 0.10 SIDE_CHAIN REMARK 500 DG A 4 0.05 SIDE_CHAIN REMARK 500 DA A 5 0.10 SIDE_CHAIN REMARK 500 DC A 6 0.22 SIDE_CHAIN REMARK 500 DG A 8 0.08 SIDE_CHAIN REMARK 500 DA A 10 0.15 SIDE_CHAIN REMARK 500 DA A 12 0.08 SIDE_CHAIN REMARK 500 DG A 16 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL

DBREF 229D A 1 17 PDB 229D 229D 1 17

SEQRES 1 A 17 DC DC DA DG DA DC UMP DG DA DA MG1 DA UMP SEQRES 2 A 17 5CM UMP DG DG

MODRES 229D UMP A 7 U 2'-DEOXYURIDINE 5'-MONOPHOSPHATE MODRES 229D MG1 A 11 DG MODRES 229D UMP A 13 U 2'-DEOXYURIDINE 5'-MONOPHOSPHATE MODRES 229D 5CM A 14 DC MODRES 229D UMP A 15 U 2'-DEOXYURIDINE 5'-MONOPHOSPHATE

HET UMP A 7 29 HET MG1 A 11 36 HET UMP A 13 29 HET 5CM A 14 33 HET UMP A 15 29

HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETNAM MG1 2'-DEOXY-1-METHYLGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

HETSYN UMP DUMP

FORMUL 1 UMP 3(C9 H13 N2 O8 P) FORMUL 1 MG1 C11 H16 N5 O7 P FORMUL 1 5CM C10 H16 N3 O7 P

LINK O3' DC A 6 P UMP A 7 1555 1555 1.60 LINK O3' UMP A 7 P DG A 8 1555 1555 1.62 LINK O3' DA A 10 P MG1 A 11 1555 1555 1.62 LINK O3' MG1 A 11 P DA A 12 1555 1555 1.62 LINK O3' DA A 12 P UMP A 13 1555 1555 1.62 LINK O3' UMP A 13 P 5CM A 14 1555 1555 1.62 LINK O3' 5CM A 14 P UMP A 15 1555 1555 1.62 LINK O3' UMP A 15 P DG A 16 1555 1555 1.62

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