1ZYF - Header Asymmetric Unit

HEADER DNA 10-JUN-05 1ZYF

TITLE STRUCTURE OF A SUPERCOILING RESPONSIVE DNA SITE

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

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID-SUPPORT PHOSPHORAMIDITE CHEMISTRY

KEYWDS DNA, SUPERCOILING, HIX, RECOMBINASE, HIN

EXPDTA SOLUTION NMR

NUMMDL 26

MDLTYP MINIMIZED AVERAGE

AUTHOR S.H.BAE,S.H.YUN,D.SUN,H.M.LIM,B.S.CHOI

REVDAT 2 24-FEB-09 1ZYF 1 VERSN REVDAT 1 23-MAY-06 1ZYF 0

JRNL AUTH S.H.BAE,S.H.YUN,D.SUN,H.M.LIM,B.S.CHOI JRNL TITL STRUCTURAL AND DYNAMIC BASIS OF A JRNL TITL 2 SUPERCOILING-RESPONSIVE DNA ELEMENT JRNL REF NUCLEIC ACIDS RES. V. 34 254 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16414956 JRNL DOI 10.1093/NAR/GKJ428

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR XPLOR-NIH REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

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

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-05. REMARK 100 THE RCSB ID CODE IS RCSB033266.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 10MM SODIUM PHOSPHATE, 100MM REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM SODIUM PHOSPHATE (PH REMARK 210 6.8), 100MM NACL; 10MM SODIUM REMARK 210 PHOSPHATE (PH 6.8), 100MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, 2D COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA, DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1995, MARDIGRAS 3.2, REMARK 210 VNMR 3.1C, X-PLOR XPLOR-NIH REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS (XPLOR-NIH) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 26 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND REMARK 210 ENERGY, STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA B 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 16 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 18 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 22 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 23 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA B 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC B 16 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA B 18 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 21 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT B 22 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT B 23 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG B 24 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 624 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZYG RELATED DB: PDB REMARK 900 HIX-CG REMARK 900 RELATED ID: 1ZYH RELATED DB: PDB REMARK 900 HIX-AG

DBREF 1ZYF A 1 12 PDB 1ZYF 1ZYF 1 12 DBREF 1ZYF B 13 24 PDB 1ZYF 1ZYF 13 24

SEQRES 1 A 12 DC DA DA DC DC DA DT DG DG DT DT DG SEQRES 1 B 12 DC DA DA DC DC DA DT DG DG DT DT DG

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