HEADER DNA 06-DEC-22 8HMW TITLE DOUBLE METHYL MODIFICATION ON GUANOSINE PROMOTES UNUSUAL STRUCTURAL TITLE 2 DISTORTION AND CONFORMATIONAL TRANSITION IN Z-DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*(SJO)P*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DNA MOLECULE; SOURCE 4 ORGANISM_TAXID: 2853804 KEYWDS METHYLATION, Z-DNA, GUANOSINE, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.-H.LEE,K.-I.OH REVDAT 3 15-MAY-24 8HMW 1 REMARK REVDAT 2 08-NOV-23 8HMW 1 JRNL REVDAT 1 26-APR-23 8HMW 0 JRNL AUTH K.-I.OH,J.-H.LEE JRNL TITL ENTROPY-DRIVEN CONFORMATIONAL TRANSITION OF FLEXIBLE Z-DNA JRNL TITL 2 TO A NOVEL NON-B HELIX BY DOUBLE-METHYLATED GUANOSINE JRNL REF J MOL LIQ 2023 JRNL REFN ESSN 1873-3166 JRNL DOI 10.1016/J.MOLLIQ.2023.122071 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRFAM-SPARKY REMARK 3 AUTHORS : WOONGHEE LEE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WITH XPLOR-NIH REMARK 4 REMARK 4 8HMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300033835. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283.15 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2 MM NA DEOXYNUCLEASE, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DD2; AVANCE III HD; AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : AGILENT; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, VNMRJ REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 5 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 5 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 5 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 5 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 200 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36526 RELATED DB: BMRB REMARK 900 DOUBLE METHYL MODIFICATION ON GUANOSINE PROMOTES UNUSUAL STRUCTURAL REMARK 900 DISTORTION AND CONFORMATIONAL TRANSITION IN Z-DNA DBREF 8HMW A 1 6 PDB 8HMW 8HMW 1 6 DBREF 8HMW B 11 16 PDB 8HMW 8HMW 11 16 SEQRES 1 A 6 DC DG DC SJO DC DG SEQRES 1 B 6 DC DG DC SJO DC DG HET SJO A 4 40 HET SJO B 14 40 HETNAM SJO [(2R,3R,4R,5R)-5-(2-AZANYL-8-METHYL-6-OXIDANYLIDENE-1H- HETNAM 2 SJO PURIN-9-YL)-4-METHOXY-3-OXIDANYL-OXOLAN-2-YL]METHYL HETNAM 3 SJO DIHYDROGEN PHOSPHATE FORMUL 1 SJO 2(C12 H18 N5 O8 P) LINK O3' DC A 3 P SJO A 4 1555 1555 1.61 LINK O3' SJO A 4 P DC A 5 1555 1555 1.61 LINK O3' DC B 13 P SJO B 14 1555 1555 1.61 LINK O3' SJO B 14 P DC B 15 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 70 92 CONECT 92 70 93 94 95 CONECT 93 92 CONECT 94 92 CONECT 95 92 99 CONECT 96 98 117 118 119 CONECT 97 98 102 115 120 CONECT 98 96 97 CONECT 99 95 100 121 122 CONECT 100 99 101 115 123 CONECT 101 100 102 CONECT 102 97 101 103 124 CONECT 103 102 104 113 CONECT 104 103 105 111 CONECT 105 104 106 CONECT 106 105 107 108 CONECT 107 106 125 126 CONECT 108 106 109 127 CONECT 109 108 110 111 CONECT 110 109 CONECT 111 104 109 112 CONECT 112 111 113 CONECT 113 103 112 114 CONECT 114 113 128 129 130 CONECT 115 97 100 116 131 CONECT 116 115 132 CONECT 117 96 CONECT 118 96 CONECT 119 96 CONECT 120 97 CONECT 121 99 CONECT 122 99 CONECT 123 100 CONECT 124 102 CONECT 125 107 CONECT 126 107 CONECT 127 108 CONECT 128 114 CONECT 129 114 CONECT 130 114 CONECT 131 115 CONECT 132 116 CONECT 266 288 CONECT 288 266 289 290 291 CONECT 289 288 CONECT 290 288 CONECT 291 288 295 CONECT 292 294 313 314 315 CONECT 293 294 298 311 316 CONECT 294 292 293 CONECT 295 291 296 317 318 CONECT 296 295 297 311 319 CONECT 297 296 298 CONECT 298 293 297 299 320 CONECT 299 298 300 309 CONECT 300 299 301 307 CONECT 301 300 302 CONECT 302 301 303 304 CONECT 303 302 321 322 CONECT 304 302 305 323 CONECT 305 304 306 307 CONECT 306 305 CONECT 307 300 305 308 CONECT 308 307 309 CONECT 309 299 308 310 CONECT 310 309 324 325 326 CONECT 311 293 296 312 327 CONECT 312 311 328 CONECT 313 292 CONECT 314 292 CONECT 315 292 CONECT 316 293 CONECT 317 295 CONECT 318 295 CONECT 319 296 CONECT 320 298 CONECT 321 303 CONECT 322 303 CONECT 323 304 CONECT 324 310 CONECT 325 310 CONECT 326 310 CONECT 327 311 CONECT 328 312 MASTER 140 0 2 0 0 0 0 6 246 2 84 2 END