HEADER DNA 28-JUN-23 8PMB TITLE MINIMAL I-MOTIF COMPRISING THREE CYTOSINE-CYTOSINE+ BASE-PAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MINIMAL I-MOTIF C21T333; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS I-MOTIF, SPECTROSCOPY, MINIMAL, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.GHEZZO,M.TRAJKOVSKI,J.PLAVEC,C.SISSI REVDAT 3 18-OCT-23 8PMB 1 JRNL REVDAT 2 11-OCT-23 8PMB 1 JRNL REVDAT 1 13-SEP-23 8PMB 0 JRNL AUTH M.GHEZZO,M.TRAJKOVSKI,J.PLAVEC,C.SISSI JRNL TITL A SCREENING PROTOCOL FOR EXPLORING LOOP LENGTH REQUIREMENTS JRNL TITL 2 FOR THE FORMATION OF A THREE CYTOSINE-CYTOSINE + BASE-PAIRED JRNL TITL 3 I-MOTIF. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 62 09327 2023 JRNL REFN ESSN 1521-3773 JRNL PMID 37611164 JRNL DOI 10.1002/ANIE.202309327 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8PMB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131545. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 0.5 MM DNA 5'-(CCTTTCTTTCCTTTC) REMARK 210 -3', 25 MM NA PHOSPHATE, 90% H2O/ REMARK 210 10% D2O; 0.5 MM 13C, 15N DNA 5'- REMARK 210 (CCTTTCTTTCCTTTC)-3', 25 MM NA REMARK 210 PHOSPHATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D 1H-13C HSQC; 2D 1H REMARK 210 -15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; UNIFORM NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 10 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 14 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DC A 15 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 15 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DC A 2 N3 - C2 - O2 ANGL. DEV. = -6.3 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 10 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 14 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT A 14 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DC A 15 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 15 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 3 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 245 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34830 RELATED DB: BMRB REMARK 900 I-MOTIF C21T333 DBREF 8PMB A 1 15 PDB 8PMB 8PMB 1 15 SEQRES 1 A 15 DC DC DT DT DT DNR DT DT DT DC DNR DT DT SEQRES 2 A 15 DT DC HET DNR A 6 31 HET DNR A 11 31 HETNAM DNR 2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 DNR 2(C9 H15 N3 O7 P 1+) LINK O3' DT A 5 P DNR A 6 1555 1555 1.60 LINK O3' DNR A 6 P DT A 7 1555 1555 1.61 LINK O3' DC A 10 P DNR A 11 1555 1555 1.62 LINK O3' DNR A 11 P DT A 12 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 CONECT 131 155 CONECT 155 131 156 157 158 CONECT 156 155 CONECT 157 155 CONECT 158 155 159 CONECT 159 158 160 174 175 CONECT 160 159 161 172 176 CONECT 161 160 162 CONECT 162 161 163 171 177 CONECT 163 162 164 165 CONECT 164 163 170 178 CONECT 165 163 166 167 CONECT 166 165 CONECT 167 165 168 179 CONECT 168 167 169 170 CONECT 169 168 180 181 CONECT 170 164 168 182 CONECT 171 162 172 183 184 CONECT 172 160 171 173 185 CONECT 173 172 186 CONECT 174 159 CONECT 175 159 CONECT 176 160 CONECT 177 162 CONECT 178 164 CONECT 179 167 CONECT 180 169 CONECT 181 169 CONECT 182 170 CONECT 183 171 CONECT 184 171 CONECT 185 172 CONECT 186 173 CONECT 290 312 CONECT 312 290 313 314 315 CONECT 313 312 CONECT 314 312 CONECT 315 312 316 CONECT 316 315 317 331 332 CONECT 317 316 318 329 333 CONECT 318 317 319 CONECT 319 318 320 328 334 CONECT 320 319 321 322 CONECT 321 320 327 335 CONECT 322 320 323 324 CONECT 323 322 CONECT 324 322 325 336 CONECT 325 324 326 327 CONECT 326 325 337 338 CONECT 327 321 325 339 CONECT 328 319 329 340 341 CONECT 329 317 328 330 342 CONECT 330 329 343 CONECT 331 316 CONECT 332 316 CONECT 333 317 CONECT 334 319 CONECT 335 321 CONECT 336 324 CONECT 337 326 CONECT 338 326 CONECT 339 327 CONECT 340 328 CONECT 341 328 CONECT 342 329 CONECT 343 330 MASTER 146 0 2 0 0 0 0 6 291 1 66 2 END