1EVO - Header Asymmetric Unit

HEADER DNA 20-APR-00 1EVO

TITLE NMR OBSERVATION OF A NOVEL C-TETRAD

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3'); COMPND 3 CHAIN: O, P, Q, R; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PARALLEL STRANDED DNA QUDRUPLEX COMPND 6 INCORPORATING C-TETRAD

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES

KEYWDS NMR STRUCTURE; G-QUADRUPLEX; C-TETRAD; GGGCGG REPEAT, SV40, KEYWDS 2 DNA

EXPDTA SOLUTION NMR

NUMMDL 10

AUTHOR P.K.PATEL,N.S.BHAVESH,R.V.HOSUR

REVDAT 2 24-FEB-09 1EVO 1 VERSN REVDAT 1 01-MAY-00 1EVO 0

JRNL AUTH P.K.PATEL,N.S.BHAVESH,R.V.HOSUR JRNL TITL NMR OBSERVATION OF A NOVEL C-TETRAD IN THE JRNL TITL 2 STRUCTURE OF THE SV40 REPEAT SEQUENCE GGGCGG. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 270 967 2000 JRNL REFN ISSN 0006-291X JRNL PMID 10772934 JRNL DOI 10.1006/BBRC.2000.2479

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : IRMA 2.3 REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AFTER SIMULATED ANNEALING-RESTRAINED REMARK 3 MOLECULAR DYNAMICS 16 STRUCTURES FOR THE QUADRUPLEX WERE REMARK 3 SELECTED ON THE BASIS OF PROPER COVALENT GEOMETRIES, REMARK 3 SYMMETRIES AND LOW ENERGIES FOR RELAXATION MATRIX REFINEMENT REMARK 3 USING IRMA (ITERATIVE RELXATION MATRIX ANALYSIS) PROTOCOL IN REMARK 3 DISCOVER. THE INPUT DATA INCLUDED NOES FROM 80, 120, 200 AND REMARK 3 300 MS NOESY SPECTRA. THREE TO FOUR SETS OF CALCULATIONS WERE REMARK 3 PERFORMED BY CHOOSING DIFFERENT REFERENCE PEAKS FOR INTENSITY REMARK 3 NORMALIZATIONS. THE ISOTROPIC CORRELATION TIME WAS OPTIMIZED REMARK 3 FOR BEST NOE FITS, WHICH YIELDED A VALUE OF 5.0 NS.FINALLY 10 REMARK 3 CONVERGENT QUADRUPLEX STRUCTURES WERE SELECTED ON THE BASIS OF REMARK 3 R1-FACTOR AND SYMMETRY

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

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-00. REMARK 100 THE RCSB ID CODE IS RCSB010933.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL; NULL REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 10 MM SODIUM PHOSPHATE, 0.2 REMARK 210 MM EDTA AND 200 MM NACL; 10 MM REMARK 210 SODIUM PHOSPHATE, 0.2 MM EDTA REMARK 210 AND 200 MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, FELIX 230 AND 97, REMARK 210 DISCOVER 3.1 REMARK 210 METHOD USED : RELAXAXTION MATRIX REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: TEMPERATYRE DEPENDENT 1D SPECTRA. TEMPERATURE WAS REMARK 210 VARIED BETWEEN -5 AND 50 C

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 DC O 305 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT O 308 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT O 308 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG P 104 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC P 105 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT P 108 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT P 108 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT Q 201 N1 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DG Q 202 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG Q 204 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT Q 208 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG R 404 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC R 405 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT R 408 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT R 408 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG O 302 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG O 304 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DC O 305 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT O 308 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT O 308 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DG P 104 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC P 105 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT P 108 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT P 108 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DG Q 202 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DT Q 208 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT Q 208 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DG R 404 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DT R 408 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT R 408 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 DG O 304 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 3 DC O 305 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DT O 308 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DT O 308 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 DG P 104 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 3 DC P 105 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT P 108 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DT P 108 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 DT Q 208 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DT Q 208 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 DG R 402 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 3 DG R 404 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 3 DT R 408 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT R 408 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 4 DT O 301 N1 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 4 DG O 302 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 4 DC O 305 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DT O 308 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DT O 308 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 4 DT P 101 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 154 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL

DBREF 1EVO O 301 308 PDB 1EVO 1EVO 301 308 DBREF 1EVO P 101 108 PDB 1EVO 1EVO 101 108 DBREF 1EVO Q 201 208 PDB 1EVO 1EVO 201 208 DBREF 1EVO R 401 408 PDB 1EVO 1EVO 401 408

SEQRES 1 O 8 DT DG DG DG DC DG DG DT SEQRES 1 P 8 DT DG DG DG DC DG DG DT SEQRES 1 Q 8 DT DG DG DG DC DG DG DT SEQRES 1 R 8 DT DG DG DG DC DG DG DT

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