225D - Header Asymmetric Unit

HEADER DNA 12-JUL-95 225D

TITLE A TETRAMERIC DNA STRUCTURE WITH PROTONATED TITLE 2 CYTOSINE:CYTOSINE BASE PAIRS

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*CP*CP*CP*C)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES

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

KEYWDS DNA, NMR, INTERCALATED CYTOSINE TETRAD

EXPDTA SOLUTION NMR

AUTHOR K.GEHRING,J.L.LEROY,M.GUERON

REVDAT 3 24-FEB-09 225D 1 VERSN REVDAT 2 01-APR-03 225D 1 JRNL REVDAT 1 15-OCT-95 225D 0

JRNL AUTH K.GEHRING,J.L.LEROY,M.GUERON JRNL TITL A TETRAMERIC DNA STRUCTURE WITH PROTONATED JRNL TITL 2 CYTOSINE.CYTOSINE BASE PAIRS. JRNL REF NATURE V. 363 561 1993 JRNL REFN ISSN 0028-0836 JRNL PMID 8389423 JRNL DOI 10.1038/363561A0

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE CALCULATION: MOLECULAR REMARK 3 DYNAMICS AND ENERGY MINIMIZATION USING X-PLOR CONSTRAINTS (PER REMARK 3 STRAND): TOTAL 70 DISTANCE CONSTRAINTS (ABOUT 12/NUCLEOTIDE) REMARK 3 43 FROM INTRANUCLEOTIDE NOES 6 FROM SEQUENTIAL INTERNUCLEOTIDE REMARK 3 NOES 21 FROM NON-SEQUENTIAL INTERNUCLEOTIDE NOES 15 FROM REMARK 3 HYDROGEN BONDS DIHEDRAL ANGLE CONSTRAINTS 10 BACKBONE AND REMARK 3 SUGAR RING TORSION ANGLES CONSTRAINTS TO MAKE CYTOSINE BASE REMARK 3 PAIRS PLANAR 4-FOLD SYMMETRY CONSTRAINTS (AS 3 SETS OF REMARK 3 PAIRWISE NON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS)

REMARK 4 REMARK 4 225D 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) : 298 REMARK 210 PH : 4.3 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 : MOLECULAR DYNAMICS, ENERGY REMARK 210 MINIMIZATION 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: DATA COLLECTION PARAMETERS: FREQUENCY: 600 MHZ FOR 1H, REMARK 210 242 MHZ FOR 31P SAMPLE TUBE: 5 MM, 7.5 MILLIMOLAR STRAND, PH REMARK 210 4.3, 25 C SPECTRA FOR ASSIGNMENTS: HOMONUCLEAR PROTON 2D, 1H- REMARK 210 31P TOCSY; SPECTRA FOR CONSTRAINTS: NOESY, DQF-COSY, 1H-31P REMARK 210 COSY

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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC B 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC B 6 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT C 1 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC C 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC C 6 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT D 1 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT D 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC D 2 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 3.8 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 DT A 1 0.07 SIDE_CHAIN REMARK 500 DT B 1 0.07 SIDE_CHAIN REMARK 500 DT C 1 0.07 SIDE_CHAIN REMARK 500 DT D 1 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL

DBREF 225D A 1 6 PDB 225D 225D 1 6 DBREF 225D B 1 6 PDB 225D 225D 1 6 DBREF 225D C 1 6 PDB 225D 225D 1 6 DBREF 225D D 1 6 PDB 225D 225D 1 6

SEQRES 1 A 6 DT DC DC DC DC DC SEQRES 1 B 6 DT DC DC DC DC DC SEQRES 1 C 6 DT DC DC DC DC DC SEQRES 1 D 6 DT DC DC DC DC DC

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