10 20 30 40 50 60 70 80 1KBM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 06-NOV-01 1KBM
TITLE SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6- TITLE 2 THIOGUANINE 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, KEYWDS 2 DOUBLE HELIX, B-FORM DNA
EXPDTA SOLUTION NMR
AUTHOR J.BOHON,C.R.DE LOS SANTOS
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 JRNL TITL 2 6-THIOGUANINE ON 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 1
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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-01. REMARK 100 THE RCSB ID CODE IS RCSB014782.
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 REMARK 210 PHOSPHATE BUFFER, 50MM NACL, REMARK 210 0.5MM EDTA REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM DNA, 25MM PHOSPHATE REMARK 210 BUFFER, 50MM NACL, 0.5MM EDTA; REMARK 210 2MM DNA, 25MM PHOSPHATE REMARK 210 BUFFER, 50MM NACL, 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 REMARK 210 BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND REMARK 210 FURTHER REFINED BY THE FULL-RELAXATION MATRIX BACK-CALCULATION REMARK 210 METHOD. 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM REMARK 210 DNA STARTING STRUCTURES. FIVE DIFFERENT STARTING TEMPERATURES REMARK 210 AND THREE DIFFERENT LENGTHS OF TIME SPENT AT THE HIGH- REMARK 210 TEMPERATURE STEP MAKE UP THE 15 STRUCTURES. 29 OF THE 30 TOTAL REMARK 210 STRUCTURES CONVERGED TO AN RMSD OF .52A OR LESS. THE AVERAGE REMARK 210 OF THESE 29 STRUCTURES WAS CALCULATED AND UTILIZED IN THE FULL REMARK 210 RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE REMARK 210 STRUCTURE FROM THIS LAST STEP IS THE FORM THAT IS DEPOSITED REMARK 210 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 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- REMARK 900 THIOGUANINE 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