HEADER DNA 01-JAN-07 2OEY TITLE SOLUTION STRUCTURE OF A DESIGNED SPIROCYCLIC HELICAL LIGAND BINDING AT TITLE 2 A TWO-BASE BULGE SITE IN DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (25-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS IS AN ARTIFICAL SEQUENCE KEYWDS DESIGNED SPIROCYCLIC HELICAL LIGAND-BULGED DNA COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR N.ZHANG,Y.LIN,Z.XIAO,G.B.JONES,I.H.GOLDBERG REVDAT 5 27-DEC-23 2OEY 1 REMARK REVDAT 4 16-MAR-22 2OEY 1 REMARK REVDAT 3 24-FEB-09 2OEY 1 VERSN REVDAT 2 01-MAY-07 2OEY 1 JRNL REVDAT 1 10-APR-07 2OEY 0 JRNL AUTH N.ZHANG,Y.LIN,Z.XIAO,G.B.JONES,I.H.GOLDBERG JRNL TITL SOLUTION STRUCTURE OF A DESIGNED SPIROCYCLIC HELICAL LIGAND JRNL TITL 2 BINDING AT A TWO-BASE BULGE SITE IN DNA. JRNL REF BIOCHEMISTRY V. 46 4793 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17388570 JRNL DOI 10.1021/BI602599D REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.STASSINOPOULOS,J.JI,X.GAO,I.H.GOLDBERG REMARK 1 TITL SOLUTION STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED WITH AN REMARK 1 TITL 2 ENEDIYNE CLEAVING ANALOGUE REMARK 1 REF SCIENCE V. 272 1943 1996 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 8658168 REMARK 1 DOI 10.1126/SCIENCE.272.5270.1943 REMARK 1 REFERENCE 2 REMARK 1 AUTH X.GAO,A.STASSINOPOLOUS,J.JI,Y.KWON,S.BARE,I.H.GOLDBERG REMARK 1 TITL INDUCED FORMATION OF A DNA BULGE STRUCTURE BY A MOLECULAR REMARK 1 TITL 2 WEDGE LIGAND-POST ACTIVATED NEOCARZINOSTATIN CHROMOPHORE REMARK 1 REF BIOCHEMISTRY V. 41 5131 2002 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 11955061 REMARK 1 DOI 10.1021/BI012112O REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 531 RESTRAINTS, 506 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE CONSTRAINTS, 25 DIHEDRAL ANGLE RESTRAINTS,40 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 2OEY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041050. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 283; 298; 303 REMARK 210 PH : 6.8; 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL; 100 MM REMARK 210 NACL; 100 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM PHOSPHATE BUFFER; 100 MM REMARK 210 NACL; 10MM PHOSPHATE BUFFER; 100 REMARK 210 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 : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000 REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD METHODS FOR REMARK 210 DNA-DRUG COMPLEX. 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 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 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 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 2 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA A 3 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT A 4 O4' - C4' - C3' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DT A 4 C1' - O4' - C4' ANGL. DEV. = -9.6 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DC A 5 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DC A 5 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC A 5 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG A 6 C3' - C2' - C1' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 7 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DT A 7 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC A 8 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 9 C3' - C2' - C1' ANGL. DEV. = -9.9 DEGREES REMARK 500 1 DT A 9 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 10 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 11 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DC A 11 C3' - C2' - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DC A 11 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 12 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC A 12 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC A 12 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 13 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DT A 13 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 14 O4' - C4' - C3' ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 14 C3' - C2' - C1' ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DT A 14 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 15 C3' - C2' - C1' ANGL. DEV. = -9.4 DEGREES REMARK 500 1 DT A 15 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 16 C3' - C2' - C1' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DG A 17 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 17 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 17 C3' - C2' - C1' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 18 C3' - C2' - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DT A 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 19 C3' - C2' - C1' ANGL. DEV. = -8.1 DEGREES REMARK 500 1 DA A 19 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 513 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE S2A A 26 DBREF 2OEY A 1 25 PDB 2OEY 2OEY 1 25 SEQRES 1 A 25 DC DC DA DT DC DG DT DC DT DA DC DC DT SEQRES 2 A 25 DT DT DG DG DT DA DG DG DA DT DG DG HET S2A A 26 73 HETNAM S2A (1R,3A'S,10'S,10A'R)-7-METHOXY-2-OXO-10',10A'-DIHYDRO- HETNAM 2 S2A 2H,3A'H-SPIRO[NAPHTHALENE-1,3'-PENTALENO[1,2- HETNAM 3 S2A B]NAPHTHALEN]-10'-YL 2,6-DIDEOXY-2-(METHYLAMINO)- HETNAM 4 S2A ALPHA-D-GALACTOPYRANOSIDE HETSYN S2A SPIROCYCLIC ALKENE FORMUL 2 S2A C33 H33 N O6 SITE 1 AC1 5 DG A 6 DT A 7 DC A 8 DG A 20 SITE 2 AC1 5 DG A 21 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 MODEL 1