HEADER DNA 02-APR-98 1A84 TITLE NMR SOLUTION STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS- TITLE 2 DIAMMINEPLATINUM(II) D(GPG) INTRASTRAND CROSS-LINK, THE MAJOR ADDUCT TITLE 3 OF THE ANTICANCER DRUG CISPLATIN, 1 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA D(CCTCTG*G*TCTCC); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CISPLATIN INTRASTRAND CROSS-LINKED DNA; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA D(GGAGACCAGAGG); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: CISPLATIN INTRASTRAND CROSS-LINKED DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, CISPLATIN, DNA, DUPLEX, DODECAMER, HMG-DOMAIN KEYWDS 2 INTERACTION EXPDTA SOLUTION NMR AUTHOR A.GELASCO,S.J.LIPPARD REVDAT 5 10-APR-24 1A84 1 REMARK LINK REVDAT 4 13-JUL-11 1A84 1 VERSN REVDAT 3 23-JUN-10 1A84 1 FORMUL REVDAT 2 24-FEB-09 1A84 1 VERSN REVDAT 1 25-NOV-98 1A84 0 JRNL AUTH A.GELASCO,S.J.LIPPARD JRNL TITL NMR SOLUTION STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING JRNL TITL 2 A CIS-DIAMMINEPLATINUM(II) D(GPG) INTRASTRAND CROSS-LINK, JRNL TITL 3 THE MAJOR ADDUCT OF THE ANTICANCER DRUG CISPLATIN. JRNL REF BIOCHEMISTRY V. 37 9230 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9649303 JRNL DOI 10.1021/BI973176V 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: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1A84 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170511. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : D2O/H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D1HNOESY; TOCSY; PECOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : FBML 750 REMARK 210 SPECTROMETER MANUFACTURER : FRANCIS BITTER MAGNET LAB CUSTOM REMARK 210 BUILT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR, QUANTA REMARK 210 METHOD USED : NOE-RESTRAINED REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D 1H-1H NMR REMARK 210 SPECTROSCOPY IN BOTH D2O AND H2O SOLUTIONS 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 H4' DA B 15 OP1 DG B 16 1.48 REMARK 500 H2'' DG B 23 OP2 DG B 24 1.57 REMARK 500 H2'' DT A 10 OP2 DC A 11 1.60 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 8 C5' DT A 8 C4' 0.048 REMARK 500 DT A 10 C5 DT A 10 C7 0.038 REMARK 500 DC A 12 C5' DC A 12 C4' 0.059 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 DC A 1 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT A 5 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DT A 5 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 11 C4' - C3' - C2' ANGL. DEV. = 5.7 DEGREES REMARK 500 DC A 11 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 12 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 DC A 12 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 13 C4' - C3' - C2' ANGL. DEV. = 6.1 DEGREES REMARK 500 DG B 13 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DG B 14 C4' - C3' - C2' ANGL. DEV. = 5.4 DEGREES REMARK 500 DG B 14 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG B 14 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA B 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 15 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 16 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 16 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG B 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA B 17 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 17 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 18 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC B 19 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 20 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 20 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 20 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG B 21 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 21 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG B 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA B 22 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA B 22 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 23 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG B 23 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 23 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG B 23 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG B 24 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 DG B 24 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 24 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 52 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 DC A 9 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 13 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 6 N7 REMARK 620 2 CPT A 13 N1 179.9 REMARK 620 3 CPT A 13 N2 89.8 90.1 REMARK 620 4 DG A 7 N7 90.1 90.0 179.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT A 13 DBREF 1A84 A 1 12 PDB 1A84 1A84 1 12 DBREF 1A84 B 13 24 PDB 1A84 1A84 13 24 SEQRES 1 A 12 DC DC DT DC DT DG DG DT DC DT DC DC SEQRES 1 B 12 DG DG DA DG DA DC DC DA DG DA DG DG HET CPT A 13 9 HETNAM CPT CISPLATIN HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 3 CPT CL2 H6 N2 PT LINK N7 DG A 6 PT1 CPT A 13 1555 1555 2.05 LINK N7 DG A 7 PT1 CPT A 13 1555 1555 2.05 SITE 1 AC1 3 DT A 5 DG A 6 DG A 7 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