HEADER DNA 25-MAY-22 7ZYX TITLE DIMERIC I-MOTIF FROM 2'FARABINOCYTIDINE-MODIFIED TC5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*(CFL)P*(CFL)P*(CFL)P*(CFL)P*(CFL))-3'); COMPND 3 CHAIN: A, B; 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, FANA, 2'FARABINOCYTIDINE, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.GARAVIS,R.EL KHOURY,M.J.DAMHA,C.GONZALEZ REVDAT 1 01-MAR-23 7ZYX 0 JRNL AUTH R.EL-KHOURY,V.MACALUSO,C.HENNECKER,A.K.MITTERMAIER,M.OROZCO, JRNL AUTH 2 C.GONZALEZ,M.GARAVIS,M.J.DAMHA JRNL TITL I-MOTIF FOLDING INTERMEDIATES WITH ZERO-NUCLEOTIDE LOOPS ARE JRNL TITL 2 TRAPPED BY 2'-FLUOROARABINOCYTIDINE VIA F···H JRNL TITL 3 AND O···H HYDROGEN BONDS. JRNL REF COMMUN CHEM V. 6 31 2023 JRNL REFN ESSN 2399-3669 JRNL PMID 36797370 JRNL DOI 10.1038/S42004-023-00831-7 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 7ZYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292123343. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 10 MM NAPI, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; 2D 1H-19F HOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, TOPSPIN, CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 45 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 38.0 KCAL/MOL 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT B 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DT B 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 7 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 8 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34735 RELATED DB: BMRB REMARK 900 DIMERIC I-MOTIF FROM 2'FARABINOCYTIDINE-MODIFIED TC5 DBREF 7ZYX A 1 6 PDB 7ZYX 7ZYX 1 6 DBREF 7ZYX B 7 12 PDB 7ZYX 7ZYX 7 12 SEQRES 1 A 6 DT CFL CFL CFL CFL CFL SEQRES 1 B 6 DT CFL CFL CFL CFL CFL HET CFL A 2 30 HET CFL A 3 30 HET CFL A 4 30 HET CFL A 5 30 HET CFL A 6 31 HET CFL B 8 30 HET CFL B 9 30 HET CFL B 10 30 HET CFL B 11 30 HET CFL B 12 31 HETNAM CFL 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D- HETNAM 2 CFL ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE HETSYN CFL 2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 CFL 10(C9 H13 F N3 O7 P) LINK O3' DT A 1 P CFL A 2 1555 1555 1.61 LINK O3' CFL A 2 P CFL A 3 1555 1555 1.61 LINK O3' CFL A 3 P CFL A 4 1555 1555 1.61 LINK O3' CFL A 4 P CFL A 5 1555 1555 1.61 LINK O3' CFL A 5 P CFL A 6 1555 1555 1.62 LINK O3' DT B 7 P CFL B 8 1555 1555 1.62 LINK O3' CFL B 8 P CFL B 9 1555 1555 1.62 LINK O3' CFL B 9 P CFL B 10 1555 1555 1.62 LINK O3' CFL B 10 P CFL B 11 1555 1555 1.62 LINK O3' CFL B 11 P CFL B 12 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 MODEL 1