HEADER DNA 09-NOV-08 2KAL TITLE NMR STRUCTURE OF FULLY METHYLATED GATC SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*DGP*DCP*DGP*DAP*DGP*(6MA)P*DTP*DCP*DTP*DGP*DCP*DG)- COMPND 3 3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*DCP*DGP*DCP*DAP*DGP*(6MA)P*DTP*DCP*DTP*DCP*DGP*DC)- COMPND 8 3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED FOLLOWING THE ESCHERICHIA COLI SOURCE 4 SEQUENCE; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: CHEMICALLY SYNTHESIZED FOLLOWING THE ESCHERICHIA COLI SOURCE 8 SEQUENCE KEYWDS GATC, N6-METHYLATED ADENINE, DNA EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR J.BANG,S.BAE,C.PARK,J.LEE,B.CHOI REVDAT 3 16-MAR-22 2KAL 1 REMARK LINK REVDAT 2 20-OCT-09 2KAL 1 HET REVDAT 1 10-FEB-09 2KAL 0 JRNL AUTH J.BANG,S.H.BAE,C.J.PARK,J.H.LEE,B.S.CHOI JRNL TITL STRUCTURAL AND DYNAMICS STUDY OF DNA DODECAMER DUPLEXES THAT JRNL TITL 2 CONTAIN UN-, HEMI-, OR FULLY METHYLATED GATC SITES. JRNL REF J.AM.CHEM.SOC. V. 130 17688 2008 JRNL REFN ISSN 0002-7863 JRNL PMID 19108701 JRNL DOI 10.1021/JA8038272 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KAL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000100883. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 287; 308; 303; 288 REMARK 210 PH : 6.8; 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL; NULL REMARK 210 PRESSURE : NULL; NULL; NULL; NULL REMARK 210 SAMPLE CONTENTS : 0.5-1.0 MM 5' REMARK 210 -D(*DGP*DCP*DGP*DAP*DGP*(6MA)P*DTP*DCP*DTP*DGP*DCP*DG)-3', 0.5- REMARK 210 1.0 MM 5'-D(*DCP*DGP*DCP*DAP*DGP*(6MA)P*DTP*DCP*DTP*DCP*DGP*DC)- REMARK 210 3', 90% H2O/10% D2O; 0.5-1.0 MM 5'-D(*DGP*DCP*DGP*DAP*DGP*(6MA)P* REMARK 210 DTP*DCP*DTP*DGP*DCP*DG)-3', 0.5-1.0 MM 5'-D(*DCP*DGP*DCP*DAP*DGP* REMARK 210 (6MA)P*DTP*DCP*DTP*DCP*DGP*DC)-3', 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H TOCSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, FELIX, NMRPIPE, NMRDRAW, REMARK 210 VNMRJ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 1 DT A 7 C5 DT A 7 C7 0.042 REMARK 500 1 DT B 19 C5 DT B 19 C7 0.041 REMARK 500 2 DT A 7 C5 DT A 7 C7 0.039 REMARK 500 2 DT B 19 C5 DT B 19 C7 0.044 REMARK 500 3 DT A 7 C5 DT A 7 C7 0.041 REMARK 500 3 DT B 19 C5 DT B 19 C7 0.041 REMARK 500 3 DT B 21 C5 DT B 21 C7 0.037 REMARK 500 4 DT A 7 C5 DT A 7 C7 0.039 REMARK 500 4 DT B 19 C5 DT B 19 C7 0.040 REMARK 500 5 DT A 7 C5 DT A 7 C7 0.039 REMARK 500 5 DT B 19 C5 DT B 19 C7 0.039 REMARK 500 5 DT B 21 C5 DT B 21 C7 0.037 REMARK 500 6 DT A 7 C5 DT A 7 C7 0.040 REMARK 500 6 DT B 19 C5 DT B 19 C7 0.041 REMARK 500 7 DT A 7 C5 DT A 7 C7 0.041 REMARK 500 7 DT B 19 C5 DT B 19 C7 0.041 REMARK 500 8 DT A 7 C5 DT A 7 C7 0.040 REMARK 500 8 DT A 9 C5 DT A 9 C7 0.036 REMARK 500 8 DT B 19 C5 DT B 19 C7 0.042 REMARK 500 9 DT A 7 C5 DT A 7 C7 0.040 REMARK 500 9 DT B 19 C5 DT B 19 C7 0.041 REMARK 500 10 DT A 7 C5 DT A 7 C7 0.041 REMARK 500 10 DT B 19 C5 DT B 19 C7 0.040 REMARK 500 11 DT A 7 C5 DT A 7 C7 0.037 REMARK 500 11 DT B 19 C5 DT B 19 C7 0.042 REMARK 500 12 DT A 7 C5 DT A 7 C7 0.040 REMARK 500 12 DT B 19 C5 DT B 19 C7 0.043 REMARK 500 12 DT B 21 C5 DT B 21 C7 0.036 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 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA B 16 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC B 22 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG B 23 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC B 24 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA B 16 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC B 20 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DT B 21 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC B 22 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG B 23 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC B 24 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 252 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KAL A 1 12 PDB 2KAL 2KAL 1 12 DBREF 2KAL B 13 24 PDB 2KAL 2KAL 13 24 SEQRES 1 A 12 DG DC DG DA DG 6MA DT DC DT DG DC DG SEQRES 1 B 12 DC DG DC DA DG 6MA DT DC DT DC DG DC MODRES 2KAL 6MA A 6 A MODRES 2KAL 6MA B 18 A HET 6MA A 6 34 HET 6MA B 18 34 HETNAM 6MA N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE FORMUL 1 6MA 2(C11 H16 N5 O6 P) LINK O3' DG A 5 P 6MA A 6 1555 1555 1.61 LINK O3' 6MA A 6 P DT A 7 1555 1555 1.61 LINK O3' DG B 17 P 6MA B 18 1555 1555 1.62 LINK O3' 6MA B 18 P DT B 19 1555 1555 1.61 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 MODEL 1