HEADER DEOXYRIBONUCLEIC ACID 19-MAY-96 1NEO OBSLTE 28-JAN-98 1NEO 2NEO TITLE NMR SOLUTION STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED TITLE 2 WITH AN ENEDIYNE CLEAVING ANALOG, 7 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA 5'-D(CCCGATCG-LINKER-GCAATTCGGG)-3'; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPLEXED WITH AN ENEDIYNE CLEAVING ANALOG SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS CARBOHYDRATE, BULGE BINDING LIGAND, ENEDIYNE ANTIBIOTIC, KEYWDS 2 ANTITUMOR AGENT, DEOXYRIBONUCLEIC ACID EXPDTA NMR, 7 STRUCTURES AUTHOR A.STASSINOPOULOS,J.JI,X.GAO,I.H.GOLDBERG REVDAT 1 07-DEC-96 1NEO 0 JRNL AUTH A.STASSINOPOULOS,J.JI,X.GAO,I.H.GOLDBERG JRNL TITL SOLUTION STRUCTURE OF A TWO-BASE DNA BULGE JRNL TITL 2 COMPLEXED WITH AN ENEDIYNE CLEAVING ANALOG JRNL REF SCIENCE V. 272 1943 1996 JRNL REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER RMS DEVIATIONS FROM IDEAL VALUES. BOND REMARK 3 LENGTHS (A) : 0.0004197 BOND ANGLES (DEGREES) : REMARK 3 1.839 DIHEDRAL ANGLES (DEGREES) : NULL IMPROPER REMARK 3 ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PLANE RESTRAINT: 0.927 REMARK 4 REMARK 4 1NEO COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-19) REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6.2 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 : 7 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 0.1M NACL, 0.01M SODIUM PHOSPHATE 0.0001M EDTA, 10 C, ~ REMARK 210 0.001M CONCENTRATION, PH 6.2 - 6.5. NOE CROSS PEAK VOLUMES REMARK 210 WERE MEASURED USING THE FELIX PROGRAM. THE ASSIGNED SPIN PAIRS REMARK 210 WERE CONVERTED TO DISTANCE RESTRAINTS USING TWO SPIN REMARK 210 APPROXIMATION. THE UPPER AND LOWER DISTANCE BOUNDS INITIALLY REMARK 210 WERE AT 50% OF THE EQUILIBRIUM DISTANCES. THE MAXIMUM REMARK 210 INTERPROTON DISTANCE WAS GENERALLY LIMITED TO 5.0 AND 5.5 FOR REMARK 210 NON-METHYL AND METHYL PROTONS, RESPECTIVELY. THE MINIMUM REMARK 210 INTERPROTON DISTANCE LIMIT WAS SET TO 1.8. DISTANCE AND SUGAR REMARK 210 CONFORMATION RESTRAINTS WERE SUPPLEMENTED BY THE INFORMATION REMARK 210 ABSTRACTED FROM OTHER DATA SETS. D DIHEDRAL ANGLES (O3'-C3'- REMARK 210 C4'- C5') OF THE DNA SUGAR MOIETIES ARE IN THE RANGE OF 110 - REMARK 210 140. THERE ARE 18 NOES INVOLVING EXCHANGEABLE PROTONS, FROM REMARK 210 WHICH A SET OF DISTANCE RESTRAINTS WAS ESTIMATED BASED ON PEAK REMARK 210 INTENSITIES (STRONG: 1.8 - 3.8, MEDIUM: 2.0 - 4.5, WEAK: 2.5 - REMARK 210 4.5). 22 DISTANCE RESTRAINTS WERE BASED ON IDEAL VALUES FOR REMARK 210 WATSON-CRICK BASE PAIRS. IN SUCCESSIVE ITERATIONS, DISTANCE REMARK 210 BOUNDS MAY BE REDUCED WHEN THE CALCULATED DISTANCES MATCH THE REMARK 210 EXPERIMENTAL RESTRAINTS. DURING THE CALCULATION, SOME REMARK 210 REPULSION DISTANCE RESTRAINTS WERE ADDED TO SEPARATE SOME REMARK 210 PROTON PAIRS (< 4 ). RELAXATION MATRIX REFINEMENTS USED THE REMARK 210 SAME SET OF DIHEDRAL ANGLE AND INTERPROTON SEPARATION REMARK 210 RESTRAINTS. THE LINKER WAS NOT INCLUDED IN THE CALCULATION. REMARK 210 DISTANCE GEOMETRY (DG), RESTRAINED MOLECULAR DYNAMICS (RMDS) REMARK 210 SIMULATIONS, AND RELAXATION MATRIX REFINEMENT WERE USED TO REMARK 210 GENERATE A FAMILY OF STRUCTURES USING THE X-PLOR PROGRAM. THE REMARK 210 NCSI-GB PARAMETER FILE WAS GENERATED FROM THE QUANTA PROGRAM REMARK 210 (MSI). NOE RESTRAINTS IN THE FORM OF SQUARE-WELL POTENTIAL AND REMARK 210 A VAN DER WAALS NON-BONDED REPULSION FUNCTION WERE USED IN THE REMARK 210 INITIAL DG EMBEDDING. TYPICAL DG CALCULATION STEPS INVOLVED REMARK 210 PARTIAL METRIZATION (USING SUBSETS PHOSPHORUS, C3', C5', C1', REMARK 210 N9, N1, C2, C4, N3, AND ALL ATOMS IN NCSI-GLU), EMBEDDING, REMARK 210 REGULARIZATION AND REFINEMENT. THE DG STRUCTURES WERE FURTHER REMARK 210 REFINED USING RMDS. A TYPICAL PROTOCOL FOR RMDS USES CLASSIC REMARK 210 FORCE FI ELDS OF NONBOND (CUTOFF 12), ELECTROSTATIC REMARK 210 (DIELECTRIC CONSTANT = 1) AND POLAR BOND INTERACTIONS (BOND REMARK 210 CUTOFF 7.5 AND ANGLE CUTOFF 80). NOES WERE NORMALLY REMARK 210 INCORPORATED AS SQUARE-WELL POTENTIAL FUNCTIONS. A BIHARMONIC REMARK 210 POTENTIAL FUNCTION WAS USED FOR THE DIHEDRAL ANGLE RESTRAINTS REMARK 210 AND THE DISTANCE RESTRAINTS RELATED TO THE WATSON-CRICK BASE REMARK 210 PAIRS. THE SHAKE ALGORITHM WITH A TOLERANCE OF 10-4 FOR BOND REMARK 210 LENGTH WAS INVOKED AT ALL STAGES OF THE CALCULATIONS. DYNAMICS REMARK 210 SIMULATIONS USING THE VERLET ALGORITHM WERE CARRIED OUT AT 1 REMARK 210 FS STEP SIZE AND TEMPERATURE WAS MAINTAINED BY COUPLING TO A REMARK 210 BATH. THE FIRST STAGE CALCULATION STARTED WITH 1000 STEPS OF REMARK 210 ENERGY MINIMIZATION, FOLLOWED BY 4 PS OF SIMULATED ANNEALING REMARK 210 DYNAMICS. DURING THIS TIME THE TEMPERATURE WAS INCREASED FROM REMARK 210 100 TO A 400 - 800 K BY 50 K INCREMENTS AND NOE FORCE REMARK 210 CONSTANTS WERE INCREASED BY A FACTOR OF 1.2 AT EACH REMARK 210 TEMPERATURE INCREMENT TO A MAXIMUM VALUE OF 100 KCAL M-1-2. 2 REMARK 210 PS EQUILIBRIUM DYNAMICS CALCULATIONS WERE PERFORMED AFTER THE REMARK 210 HEATING PROCESS, AND THE SYSTEM WAS THEN COOLED TO 300 K BY 50 REMARK 210 K DECREMENTS FOR A TOTAL OF A FEW PS (TIME LENGTH DEPENDING ON REMARK 210 THE TEMPERATURE DIFFERENTIAL BETWEEN THE INITIAL AND THE FINAL REMARK 210 STAGE). AFTER TURNING ON THE EXPERIMENTAL DIHEDRAL ANGLE REMARK 210 FUNCTION, ADDITIONAL 2 PS DYNAMICS CALCULATIONS WERE CARRIED REMARK 210 OUT, FOLLOWED BY 500 STEPS OF ENERGY MINIMIZATION TO GIVE A REMARK 210 NEW GENERATION OF CALCULATED STRUCTURES. RELAXATION MATRIX REMARK 210 REFINEMENT WAS USED IN THE FINAL STAGE TO CORRECT THE EFFECTS REMARK 210 OF SPIN DIFFUSION, WHICH CAUSES NON-LINEAR EVOLUTION OF NOE REMARK 210 INTENSITY FOR PROTONS LOCATED IN A HIGH PROTON DENSITY REMARK 210 ENVIRONMENT. TO REDUCE THE COMPUTATION TIME, NON-BOND REMARK 210 INTERACTIONS WERE MEASURED TO 9.0. PROTONS WERE DIVIDED INTO REMARK 210 THREE GROUPS: H5 AND H5, OTHER SUGAR PROTONS, AND BASE REMARK 210 PROTONS. EACH WAS ASSIGNED AN ORDER PARAMETER RANGING FROM REMARK 210 0.65 TO 0.85. A 5 NS ISOTROPIC CORRELATION TIME (T) WAS REMARK 210 DERIVED FROM A GRID RESEARCH ROUTINE USING X-PLOR. VOLUME REMARK 210 BOUNDS WERE ENTERED IN AN ABSOLUTE MODE AND EQUILIBRIUM REMARK 210 INTENSITIES AND SQUARE-WELL FUNCTIONS WERE U SED. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 1 NCS 21 REMARK 465 2 NCS 21 REMARK 465 3 NCS 21 REMARK 465 4 NCS 21 REMARK 465 5 NCS 21 REMARK 465 6 NCS 21 REMARK 465 7 NCS 21 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 1 DG 9 P OP1 OP2 REMARK 470 2 DG 9 P OP1 OP2 REMARK 470 3 DG 9 P OP1 OP2 REMARK 470 4 DG 9 P OP1 OP2 REMARK 470 5 DG 9 P OP1 OP2 REMARK 470 6 DG 9 P OP1 OP2 REMARK 470 7 DG 9 P OP1 OP2 DBREF 1NEO 1 18 PDB 1NEO 1NEO 1 18 SEQRES 1 19 NCS DC DC DC DG DA DT DG DC DG DC DA DA SEQRES 2 19 DT DT DC DG DG DG HET NCS 21 84 HETNAM NCS SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3, HETNAM 2 NCS 1'-[5-HYDROXY-9-[2-METHYLAMINO-2,6- HETNAM 3 NCS DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4- HETNAM 4 NCS YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S- HETNAM 5 NCS INDACEN-2-ONE]] FORMUL 2 NCS C35 H36 N O12 1+ 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