HEADER DNA 19-JUN-97 2NEO TITLE SOLUTION NMR STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED WITH AN TITLE 2 ENEDIYNE CLEAVING ANALOG, 11 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*CP*CP*GP*AP*TP*GP*CP*PGE*GP*CP*AP*AP*TP*TP*CP*GP*GP*G)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: NEOCARZINOSTATIN CHROMOPHORE DERIVATIVE (NCSI-GB)- COMPND 7 BULGE-D(CCCGATCG-LINKER-GCAATTCGGG) COMPLEX SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA, BULGE DNA, ENEDIYNE ANTIBIOTICS ANTITUMOR AGENTS, CARBOHYDRATES, KEYWDS 2 BULGE BINDING LIGANDS, DEOXYRIBONUCLEIC ACID EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR A.STASSINOPOULOS,J.JI,X.GAO,I.H.GOLDBERG REVDAT 4 22-MAY-24 2NEO 1 REMARK REVDAT 3 16-MAR-22 2NEO 1 REMARK REVDAT 2 24-FEB-09 2NEO 1 VERSN REVDAT 1 28-JAN-98 2NEO 0 SPRSDE 28-JAN-98 2NEO 1NEO JRNL AUTH A.STASSINOPOULOS,J.JI,X.GAO,I.H.GOLDBERG JRNL TITL SOLUTION STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED WITH AN JRNL TITL 2 ENEDIYNE CLEAVING ANALOG. JRNL REF SCIENCE V. 272 1943 1996 JRNL REFN ISSN 0036-8075 JRNL PMID 8658168 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: NULL REMARK 4 REMARK 4 2NEO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178401. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6. REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY; COSY-35; 1H-31P REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX-II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR REMARK 210 DYNAMICS SIMULATIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 7 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-11 REMARK 465 RES C SSSEQI REMARK 465 PGE A 8A REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-11 REMARK 470 RES CSSEQI ATOMS REMARK 470 DG A 9 P OP1 OP2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DC A 1 C4 DC A 1 N4 0.060 REMARK 500 1 DC A 1 N1 DC A 1 C6 -0.054 REMARK 500 1 DC A 1 C5 DC A 1 C6 0.048 REMARK 500 1 DC A 2 C4 DC A 2 N4 0.060 REMARK 500 1 DC A 2 N1 DC A 2 C6 -0.054 REMARK 500 1 DC A 2 C5 DC A 2 C6 0.049 REMARK 500 1 DC A 3 C4 DC A 3 N4 0.060 REMARK 500 1 DC A 3 N1 DC A 3 C6 -0.054 REMARK 500 1 DC A 3 C5 DC A 3 C6 0.049 REMARK 500 1 DG A 4 N1 DG A 4 C2 -0.059 REMARK 500 1 DG A 4 C4 DG A 4 C5 0.102 REMARK 500 1 DG A 4 N7 DG A 4 C8 0.042 REMARK 500 1 DA A 5 C4 DA A 5 C5 0.097 REMARK 500 1 DA A 5 C6 DA A 5 N6 0.060 REMARK 500 1 DT A 6 N3 DT A 6 C4 -0.049 REMARK 500 1 DT A 6 C4 DT A 6 C5 0.055 REMARK 500 1 DT A 6 C5 DT A 6 C6 0.047 REMARK 500 1 DT A 6 C6 DT A 6 N1 -0.064 REMARK 500 1 DG A 7 N1 DG A 7 C2 -0.060 REMARK 500 1 DG A 7 C4 DG A 7 C5 0.101 REMARK 500 1 DG A 7 N7 DG A 7 C8 0.041 REMARK 500 1 DC A 8 C4 DC A 8 N4 0.060 REMARK 500 1 DC A 8 N1 DC A 8 C6 -0.054 REMARK 500 1 DC A 8 C5 DC A 8 C6 0.048 REMARK 500 1 DG A 9 N1 DG A 9 C2 -0.060 REMARK 500 1 DG A 9 C4 DG A 9 C5 0.101 REMARK 500 1 DG A 9 N7 DG A 9 C8 0.041 REMARK 500 1 DC A 10 C4 DC A 10 N4 0.060 REMARK 500 1 DC A 10 N1 DC A 10 C6 -0.054 REMARK 500 1 DC A 10 C5 DC A 10 C6 0.048 REMARK 500 1 DA A 11 C4 DA A 11 C5 0.097 REMARK 500 1 DA A 11 C6 DA A 11 N6 0.060 REMARK 500 1 DA A 12 C4 DA A 12 C5 0.097 REMARK 500 1 DA A 12 C6 DA A 12 N6 0.060 REMARK 500 1 DT A 13 N3 DT A 13 C4 -0.050 REMARK 500 1 DT A 13 C4 DT A 13 C5 0.056 REMARK 500 1 DT A 13 C5 DT A 13 C6 0.048 REMARK 500 1 DT A 13 C6 DT A 13 N1 -0.065 REMARK 500 1 DT A 14 N3 DT A 14 C4 -0.049 REMARK 500 1 DT A 14 C4 DT A 14 C5 0.055 REMARK 500 1 DT A 14 C5 DT A 14 C6 0.048 REMARK 500 1 DT A 14 C6 DT A 14 N1 -0.065 REMARK 500 1 DC A 15 C4 DC A 15 N4 0.060 REMARK 500 1 DC A 15 N1 DC A 15 C6 -0.054 REMARK 500 1 DC A 15 C5 DC A 15 C6 0.048 REMARK 500 1 DG A 16 N1 DG A 16 C2 -0.061 REMARK 500 1 DG A 16 C4 DG A 16 C5 0.102 REMARK 500 1 DG A 16 N7 DG A 16 C8 0.042 REMARK 500 1 DG A 17 N1 DG A 17 C2 -0.060 REMARK 500 1 DG A 17 C4 DG A 17 C5 0.101 REMARK 500 REMARK 500 THIS ENTRY HAS 563 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 N1 - C2 - O2 ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DC A 2 OP1 - P - OP2 ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DC A 3 N3 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 3 N1 - C2 - O2 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DC A 3 N3 - C2 - O2 ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DG A 4 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 1 DG A 4 C2 - N3 - C4 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DG A 4 N3 - C4 - C5 ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DG A 4 C5 - C6 - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DG A 4 C4 - C5 - N7 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 4 N3 - C4 - N9 ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DG A 4 C6 - C5 - N7 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 4 N3 - C2 - N2 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG A 4 N1 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 5 N1 - C2 - N3 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 5 C2 - N3 - C4 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DA A 5 N3 - C4 - C5 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 10.1 DEGREES REMARK 500 1 DA A 5 N3 - C4 - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DA A 5 C6 - C5 - N7 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -8.3 DEGREES REMARK 500 1 DT A 6 O3' - P - O5' ANGL. DEV. = 11.8 DEGREES REMARK 500 1 DT A 6 OP1 - P - OP2 ANGL. DEV. = -10.4 DEGREES REMARK 500 1 DT A 6 N1 - C2 - N3 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DT A 6 C2 - N3 - C4 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 6 N3 - C2 - O2 ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DT A 6 N3 - C4 - O4 ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DT A 6 C4 - C5 - C7 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 7 OP1 - P - OP2 ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 7 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG A 7 N3 - C4 - C5 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 7 C5 - C6 - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 7 C4 - C5 - N7 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 7 N3 - C4 - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DG A 7 C6 - C5 - N7 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG A 7 N1 - C6 - O6 ANGL. DEV. = -8.2 DEGREES REMARK 500 1 DC A 8 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DC A 8 N1 - C2 - O2 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DC A 8 N3 - C2 - O2 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DG A 9 C2 - N3 - C4 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 9 N3 - C4 - C5 ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DG A 9 C5 - C6 - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG A 9 N3 - C4 - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1418 ANGLE DEVIATIONS. 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 1 DT A 14 0.08 SIDE CHAIN REMARK 500 2 DT A 14 0.07 SIDE CHAIN REMARK 500 3 DT A 14 0.08 SIDE CHAIN REMARK 500 4 DT A 14 0.07 SIDE CHAIN REMARK 500 5 DT A 14 0.07 SIDE CHAIN REMARK 500 6 DT A 14 0.07 SIDE CHAIN REMARK 500 7 DT A 14 0.07 SIDE CHAIN REMARK 500 8 DT A 14 0.07 SIDE CHAIN REMARK 500 9 DC A 3 0.07 SIDE CHAIN REMARK 500 9 DT A 14 0.07 SIDE CHAIN REMARK 500 10 DT A 14 0.07 SIDE CHAIN REMARK 500 11 DT A 14 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PGE: THE LINKER IS TRIETHYLENE GLYCOL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCS A 21 DBREF 2NEO A 1 18 PDB 2NEO 2NEO 1 18 SEQRES 1 A 19 DC DC DC DG DA DT DG DC PGE DG DC DA DA SEQRES 2 A 19 DT DT DC DG DG DG HET NCS A 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+ SITE 1 AC1 9 DC A 3 DG A 4 DA A 5 DT A 6 SITE 2 AC1 9 DA A 11 DA A 12 DT A 13 DT A 14 SITE 3 AC1 9 DC A 15 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