PDB Short entry for 1XRW HEADER DNA 16-OCT-04 1XRW TITLE SOLUTION STRUCTURE OF A PLATINUM-ACRIDINE MODIFIED OCTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*CP*GP*TP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*GP*AP*CP*GP*AP*GP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS PLATINUM, ACRIDINE, DUAL BINDING MODE, MAJOR GROOVE, UNWINDING, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR H.BARUAH,M.W.WRIGHT,U.BIERBACH REVDAT 3 20-APR-16 1XRW 1 FORMUL HETATM VERSN REVDAT 2 24-FEB-09 1XRW 1 VERSN REVDAT 1 03-MAY-05 1XRW 0 JRNL AUTH H.BARUAH,M.W.WRIGHT,U.BIERBACH JRNL TITL SOLUTION STRUCTURAL STUDY OF A DNA DUPLEX CONTAINING THE JRNL TITL 2 GUANINE-N7 ADDUCT FORMED BY A CYTOTOXIC PLATINUM-ACRIDINE JRNL TITL 3 HYBRID AGENT JRNL REF BIOCHEMISTRY V. 44 6059 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15835895 JRNL DOI 10.1021/BI050021B REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 2000 REMARK 3 AUTHORS : ACCELRYS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XRW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-04. REMARK 100 THE RCSB ID CODE IS RCSB030695. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10 MM NAH2PO4, 10 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3.5MM MODIFIED DUPLEX, 10 MM REMARK 210 PHOSPHATE BUFFER, 10MM NACL, 100% REMARK 210 D2O OR 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D TOCSY; 2D NOESY; 1H REMARK 210 -31P COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, FELIX 2000, REMARK 210 MARDIGRAS 3.2, CORMA 5.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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: 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: 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 DG A 5 N1 DG A 5 C2 0.090 REMARK 500 DG A 5 C6 DG A 5 N1 -0.050 REMARK 500 DG A 5 C5 DG A 5 N7 0.057 REMARK 500 DG A 5 N7 DG A 5 C8 0.132 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 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 5 C6 - N1 - C2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 5 C5 - C6 - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG A 5 C4 - C5 - N7 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 5 C5 - N7 - C8 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG A 5 C8 - N9 - C4 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 5 C6 - C5 - N7 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 5 C3' - O3' - P ANGL. DEV. = -8.4 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 5 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES 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 DG A 5 0.07 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 2PT B 20 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 5 N7 REMARK 620 2 2PT B 20 S 82.5 REMARK 620 3 2PT B 20 N5 93.1 175.7 REMARK 620 4 2PT B 20 N4 174.4 100.7 83.6 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 2PT B 20 DBREF 1XRW A 1 8 PDB 1XRW 1XRW 1 8 DBREF 1XRW B 1 8 PDB 1XRW 1XRW 1 8 SEQRES 1 A 8 DC DC DT DC DG DT DC DC SEQRES 1 B 8 DG DG DA DC DG DA DG DG HET 2PT B 20 57 HETNAM 2PT 1-[2-(ACRIDIN-9-YLAMINO)ETHYL]-1,3-DIMETHYLTHIOUREA- HETNAM 2 2PT PLATINUM(II)-ETHANE-1,2-DIAMINE FORMUL 3 2PT C20 H29 N6 PT S 3+ LINK N7 DG A 5 PT 2PT B 20 1555 1555 2.04 SITE 1 AC1 5 DC A 4 DG A 5 DT A 6 DC B 4 SITE 2 AC1 5 DG B 5 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