HEADER DNA 26-JUL-01 1JO1 TITLE N7-GUANINE ADDUCT OF 2,7-DIAMINOMITOSENE WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*GP*(DAJ)GP*TP*AP*TP*AP*CP*CP*AP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED USING ABI-380B SYNTHESIZER KEYWDS DOUBLE HELIX, MAJOR GROOVE BINDING DRUG, GUANINE-N7-ALKYLATOR, DNA EXPDTA SOLUTION NMR AUTHOR G.SUBRAMANIAM,M.M.PAZ,G.S.KUMAR,A.DAS,Y.PALOM,C.C.CLEMENT,D.J.PATEL, AUTHOR 2 M.TOMASZ REVDAT 4 23-FEB-22 1JO1 1 REMARK LINK REVDAT 3 24-FEB-09 1JO1 1 VERSN REVDAT 2 01-APR-03 1JO1 1 JRNL REVDAT 1 12-SEP-01 1JO1 0 JRNL AUTH G.SUBRAMANIAM,M.M.PAZ,G.SURESH KUMAR,A.DAS,Y.PALOM, JRNL AUTH 2 C.C.CLEMENT,D.J.PATEL,M.TOMASZ JRNL TITL SOLUTION STRUCTURE OF A GUANINE-N7-LINKED COMPLEX OF THE JRNL TITL 2 MITOMYCIN C METABOLITE 2,7-DIAMINOMITOSENE AND DNA. BASIS OF JRNL TITL 3 SEQUENCE SELECTIVITY. JRNL REF BIOCHEMISTRY V. 40 10473 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11523988 JRNL DOI 10.1021/BI010965A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, X-PLOR 3.01 REMARK 3 AUTHORS : VARIAN INSTRUMENTS (VNMR), A. BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 126 REMARK 3 INTRAMOLECULAR DNA CONSTRAINTS, 30 H-BONDING CONSTRAINTS, 48 REMARK 3 INTERMOLECULAR DRUG-DNA CONSTRAINTS, AND 48 DIHEDRAL CONSTRAINTS REMARK 4 REMARK 4 1JO1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013991. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 303 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 0.1 M NACL; 0.1 M NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM D(GTG(+G)TATACCAC) DUPLEX REMARK 210 IN 0.01 M SODIUM PHOSPHATE, 0.1 REMARK 210 M NACL, 0.001M EDTA; 1.2 MM REMARK 210 D(GTG(+G)TATACCAC) DUPLEX IN REMARK 210 0.01 M SODIUM PHOSPHATE, 0.1 M REMARK 210 NACL, 0.001M EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; P-COSY; HOHAHA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 3.0, X-PLOR 3.01 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 12 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST NUMBER OF NOE VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D-NOE REMARK 210 BUILDUP STUDIES IN H2O AND D2O BUFFERS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O4 DT B 7 HN1 DAJ A 13 1.48 REMARK 500 O4 DT A 7 HN1 DAJ B 13 1.48 REMARK 500 REMARK 500 REMARK: NULL 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 DT A 2 C5 DT A 2 C7 0.041 REMARK 500 DG A 4 N7 DG A 4 C8 0.068 REMARK 500 DT A 5 C5 DT A 5 C7 0.051 REMARK 500 DT A 7 C5 DT A 7 C7 0.038 REMARK 500 DT B 2 C5 DT B 2 C7 0.041 REMARK 500 DG B 4 N7 DG B 4 C8 0.068 REMARK 500 DT B 5 C5 DT B 5 C7 0.051 REMARK 500 DT B 7 C5 DT B 7 C7 0.037 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 DG A 4 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 4 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT A 5 C4 - C5 - C7 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -6.8 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC A 9 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DC A 9 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 2 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 DG B 4 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG B 4 N9 - C4 - C5 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT B 5 C4 - C5 - C7 ANGL. DEV. = 5.6 DEGREES REMARK 500 DT B 5 C6 - C5 - C7 ANGL. DEV. = -6.8 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 7 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC B 9 O4' - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DC B 9 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 10 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES 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 DAJ A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAJ B 13 DBREF 1JO1 A 1 12 PDB 1JO1 1JO1 1 12 DBREF 1JO1 B 1 12 PDB 1JO1 1JO1 1 12 SEQRES 1 A 12 DG DT DG DG DT DA DT DA DC DC DA DC SEQRES 1 B 12 DG DT DG DG DT DA DT DA DC DC DA DC HET DAJ A 13 33 HET DAJ B 13 33 HETNAM DAJ DECARBAMOYL-2,7-DIAMINOMITOSENE FORMUL 3 DAJ 2(C13 H16 N3 O2 1+) LINK N7 DG A 4 C10 DAJ A 13 1555 1555 1.50 LINK N7 DG B 4 C10 DAJ B 13 1555 1555 1.50 SITE 1 AC1 6 DG A 3 DG A 4 DT A 5 DA A 6 SITE 2 AC1 6 DA B 6 DT B 7 SITE 1 AC2 6 DA A 6 DT A 7 DG B 3 DG B 4 SITE 2 AC2 6 DT B 5 DA B 6 CRYST1 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