HEADER DNA 06-NOV-01 1KBM TITLE SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE TITLE 2 OPPOSITE THYMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*TP*AP*CP*(S6G)P*CP*AP*TP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*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 THIOGUANINE, 6-THIOGUANINE, TG, 6TG, S6G, THIOPURINE, DOUBLE HELIX, KEYWDS 2 B-FORM DNA, DNA EXPDTA SOLUTION NMR AUTHOR J.BOHON,C.R.DE LOS SANTOS REVDAT 4 23-FEB-22 1KBM 1 REMARK LINK REVDAT 3 24-FEB-09 1KBM 1 VERSN REVDAT 2 21-DEC-04 1KBM 1 AUTHOR JRNL EXPDTA REMARK REVDAT 2 2 1 MASTER REVDAT 1 28-NOV-01 1KBM 0 JRNL AUTH J.BOHON,C.R.DE LOS SANTOS JRNL TITL STRUCTURAL EFFECT OF THE ANTICANCER AGENT 6-THIOGUANINE ON JRNL TITL 2 DUPLEX DNA. JRNL REF NUCLEIC ACIDS RES. V. 31 1331 2003 JRNL REFN ISSN 0305-1048 JRNL PMID 12582253 JRNL DOI 10.1093/NAR/GKG203 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014782. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 276 REMARK 210 PH : 6.78; 6.78 REMARK 210 IONIC STRENGTH : 25MM PHOSPHATE BUFFER, 50MM REMARK 210 NACL, 0.5MM EDTA; 25MM PHOSPHATE REMARK 210 BUFFER, 50MM NACL, 0.5MM EDTA REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM DNA, 25MM PHOSPHATE BUFFER, REMARK 210 50MM NACL, 0.5MM EDTA; 2MM DNA, REMARK 210 25MM PHOSPHATE BUFFER, 50MM NACL, REMARK 210 0.5MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; DQFCOSY; COSY45; REMARK 210 TOCSY; HETCO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95 AND 98 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 SIMULATIONS 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: THE STRUCTURE WAS DETERMINED USING PROTON NMR FOLLOWED BY REMARK 210 DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REMARK 210 REFINED BY THE FULL-RELAXATION MATRIX BACK-CALCULATION METHOD. REMARK 210 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM DNA REMARK 210 STARTING STRUCTURES. FIVE DIFFERENT STARTING TEMPERATURES AND REMARK 210 THREE DIFFERENT LENGTHS OF TIME SPENT AT THE HIGH-TEMPERATURE REMARK 210 STEP MAKE UP THE 15 STRUCTURES. 29 OF THE 30 TOTAL STRUCTURES REMARK 210 CONVERGED TO AN RMSD OF .52A OR LESS. THE AVERAGE OF THESE 29 REMARK 210 STRUCTURES WAS CALCULATED AND UTILIZED IN THE FULL RELAXATION REMARK 210 MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM REMARK 210 THIS LAST STEP IS THE FORM THAT IS DEPOSITED HERE. 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 DC A 1 C4 DC A 1 N4 0.095 REMARK 500 DG A 2 C2 DG A 2 N2 0.080 REMARK 500 DT A 3 C5 DT A 3 C7 0.037 REMARK 500 DA A 4 C6 DA A 4 N6 0.094 REMARK 500 DC A 5 C4 DC A 5 N4 0.095 REMARK 500 DC A 7 C4 DC A 7 N4 0.095 REMARK 500 DA A 8 C6 DA A 8 N6 0.096 REMARK 500 DT A 9 C5 DT A 9 C7 0.038 REMARK 500 DG A 10 C2 DG A 10 N2 0.080 REMARK 500 DC A 11 C4 DC A 11 N4 0.093 REMARK 500 DG B 1 C2 DG B 1 N2 0.081 REMARK 500 DC B 2 C4 DC B 2 N4 0.095 REMARK 500 DA B 3 C6 DA B 3 N6 0.093 REMARK 500 DT B 4 C5 DT B 4 C7 0.036 REMARK 500 DG B 5 C2 DG B 5 N2 0.084 REMARK 500 DT B 6 C5 DT B 6 C7 0.039 REMARK 500 DG B 7 C2 DG B 7 N2 0.081 REMARK 500 DT B 8 C5 DT B 8 C7 0.037 REMARK 500 DA B 9 C6 DA B 9 N6 0.094 REMARK 500 DC B 10 C4 DC B 10 N4 0.094 REMARK 500 DG B 11 C2 DG B 11 N2 0.086 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 2 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 7 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG B 11 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KB1 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE REMARK 900 OPPOSITE CYTOSINE DBREF 1KBM A 1 11 PDB 1KBM 1KBM 1 11 DBREF 1KBM B 1 11 PDB 1KBM 1KBM 1 11 SEQRES 1 A 11 DC DG DT DA DC S6G DC DA DT DG DC SEQRES 1 B 11 DG DC DA DT DG DT DG DT DA DC DG MODRES 1KBM S6G A 6 DG HET S6G A 6 33 HETNAM S6G 6-THIO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE FORMUL 1 S6G C10 H14 N5 O6 P S LINK O3' DC A 5 P S6G A 6 1555 1555 1.62 LINK O3' S6G A 6 P DC A 7 1555 1555 1.62 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