HEADER DNA 12-JUL-17 5OGA TITLE STRUCTURE OF MINIMAL I-MOTIF DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*(DCP)P*GP*TP*TP*CP*(DCP) COMPND 3 P*GP*TP*TP*TP*TP*TP*CP*GP*TP*TP*CP*CP*GP*T)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS I-MOTIF, DNA NON-CANONICAL STRUCTURE, MINOR GROOVE TETRAD, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR B.MIR,I.SERRANO,D.BUITRAGO,M.OROZCO,N.ESCAJA,C.GONZALEZ REVDAT 3 19-JUN-24 5OGA 1 REMARK REVDAT 2 08-MAY-19 5OGA 1 REMARK REVDAT 1 29-NOV-17 5OGA 0 JRNL AUTH B.MIR,I.SERRANO,D.BUITRAGO,M.OROZCO,N.ESCAJA,C.GONZALEZ JRNL TITL PREVALENT SEQUENCES IN THE HUMAN GENOME CAN FORM MINI JRNL TITL 2 I-MOTIF STRUCTURES AT PHYSIOLOGICAL PH. JRNL REF J. AM. CHEM. SOC. V. 139 13985 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28933543 JRNL DOI 10.1021/JACS.7B07383 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 5OGA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005574. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10 MM NAPI REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM LL3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 HO5' THM A 1 OP1 DT A 10 1.38 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 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 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 DT A 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 11 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 11 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 14 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DC A 14 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 15 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 16 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC A 18 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 18 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC A 19 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC A 19 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 19 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 21 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 21 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 10 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT A 11 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DC A 14 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 14 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DG A 15 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 16 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT A 16 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 274 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DT A 13 0.06 SIDE CHAIN REMARK 500 1 DT A 16 0.06 SIDE CHAIN REMARK 500 1 DC A 18 0.08 SIDE CHAIN REMARK 500 2 DT A 13 0.07 SIDE CHAIN REMARK 500 2 DT A 16 0.07 SIDE CHAIN REMARK 500 3 DC A 18 0.07 SIDE CHAIN REMARK 500 3 DC A 19 0.06 SIDE CHAIN REMARK 500 4 DC A 18 0.17 SIDE CHAIN REMARK 500 5 DC A 6 0.11 SIDE CHAIN REMARK 500 5 DC A 18 0.08 SIDE CHAIN REMARK 500 6 DC A 6 0.09 SIDE CHAIN REMARK 500 6 DT A 11 0.07 SIDE CHAIN REMARK 500 6 DC A 18 0.10 SIDE CHAIN REMARK 500 7 DC A 18 0.06 SIDE CHAIN REMARK 500 7 DC A 19 0.06 SIDE CHAIN REMARK 500 8 DT A 13 0.06 SIDE CHAIN REMARK 500 8 DC A 18 0.14 SIDE CHAIN REMARK 500 9 DT A 10 0.07 SIDE CHAIN REMARK 500 9 DT A 13 0.07 SIDE CHAIN REMARK 500 9 DG A 20 0.05 SIDE CHAIN REMARK 500 10 DT A 9 0.10 SIDE CHAIN REMARK 500 10 DT A 16 0.10 SIDE CHAIN REMARK 500 10 DC A 18 0.07 SIDE CHAIN REMARK 500 10 DC A 19 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34162 RELATED DB: BMRB REMARK 900 STRUCTURE OF MINIMAL I-MOTIF DOMAIN DBREF 5OGA A 1 21 PDB 5OGA 5OGA 1 21 SEQRES 1 A 21 THM DNR DG DT DT DC DNR DG DT DT DT DT DT SEQRES 2 A 21 DC DG DT DT DC DC DG DT HET THM A 1 30 HET DNR A 2 31 HET DNR A 7 31 HETNAM THM THYMIDINE HETNAM DNR 2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE FORMUL 1 THM C10 H14 N2 O5 FORMUL 1 DNR 2(C9 H15 N3 O7 P 1+) LINK O3' THM A 1 P DNR A 2 1555 1555 1.61 LINK O3' DNR A 2 P DG A 3 1555 1555 1.60 LINK O3' DC A 6 P DNR A 7 1555 1555 1.59 LINK O3' DNR A 7 P DG A 8 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 HETATM 1 O5' THM A 1 31.996 20.129 17.847 1.00 0.00 O HETATM 2 C5' THM A 1 31.072 19.098 18.218 1.00 0.00 C HETATM 3 C4' THM A 1 29.642 19.601 18.492 1.00 0.00 C HETATM 4 O4' THM A 1 29.616 20.421 19.651 1.00 0.00 O HETATM 5 C3' THM A 1 29.035 20.404 17.335 1.00 0.00 C HETATM 6 O3' THM A 1 28.359 19.557 16.423 1.00 0.00 O HETATM 7 C2' THM A 1 28.098 21.351 18.082 1.00 0.00 C HETATM 8 C1' THM A 1 28.731 21.506 19.461 1.00 0.00 C HETATM 9 N1 THM A 1 29.498 22.769 19.629 1.00 0.00 N HETATM 10 C2 THM A 1 29.111 23.634 20.656 1.00 0.00 C HETATM 11 O2 THM A 1 28.125 23.430 21.363 1.00 0.00 O HETATM 12 N3 THM A 1 29.876 24.774 20.835 1.00 0.00 N HETATM 13 C4 THM A 1 30.967 25.134 20.072 1.00 0.00 C HETATM 14 O4 THM A 1 31.563 26.171 20.341 1.00 0.00 O HETATM 15 C5 THM A 1 31.287 24.208 18.991 1.00 0.00 C HETATM 16 C5M THM A 1 32.450 24.499 18.066 1.00 0.00 C HETATM 17 C6 THM A 1 30.566 23.071 18.814 1.00 0.00 C HETATM 18 HO5' THM A 1 32.637 20.389 18.612 1.00 0.00 H HETATM 19 H5'1 THM A 1 31.431 18.567 19.101 1.00 0.00 H HETATM 20 H5'2 THM A 1 31.007 18.382 17.397 1.00 0.00 H HETATM 21 H4' THM A 1 28.987 18.743 18.672 1.00 0.00 H HETATM 22 H3' THM A 1 29.806 20.965 16.810 1.00 0.00 H HETATM 23 H2'1 THM A 1 27.992 22.303 17.559 1.00 0.00 H HETATM 24 H2'2 THM A 1 27.121 20.884 18.211 1.00 0.00 H HETATM 25 H1' THM A 1 27.937 21.459 20.208 1.00 0.00 H HETATM 26 HN3 THM A 1 29.677 25.387 21.622 1.00 0.00 H HETATM 27 HM51 THM A 1 32.702 23.627 17.463 1.00 0.00 H HETATM 28 HM52 THM A 1 33.312 24.786 18.665 1.00 0.00 H HETATM 29 HM53 THM A 1 32.186 25.337 17.421 1.00 0.00 H HETATM 30 H6 THM A 1 30.846 22.378 18.035 1.00 0.00 H HETATM 31 P DNR A 2 27.466 20.143 15.216 1.00 0.00 P HETATM 32 OP1 DNR A 2 27.220 19.070 14.231 1.00 0.00 O HETATM 33 OP2 DNR A 2 28.039 21.438 14.778 1.00 0.00 O HETATM 34 O5' DNR A 2 26.094 20.426 15.993 1.00 0.00 O HETATM 35 C5' DNR A 2 25.112 21.284 15.475 1.00 0.00 C HETATM 36 C4' DNR A 2 23.918 21.253 16.435 1.00 0.00 C HETATM 37 O4' DNR A 2 24.062 22.244 17.452 1.00 0.00 O HETATM 38 C1' DNR A 2 22.895 23.039 17.474 1.00 0.00 C HETATM 39 N1 DNR A 2 23.247 24.418 17.896 1.00 0.00 N HETATM 40 C6 DNR A 2 24.234 25.140 17.259 1.00 0.00 C HETATM 41 C2 DNR A 2 22.555 24.969 18.969 1.00 0.00 C HETATM 42 O2 DNR A 2 21.701 24.376 19.622 1.00 0.00 O HETATM 43 N3 DNR A 2 22.862 26.253 19.315 1.00 0.00 N HETATM 44 C4 DNR A 2 23.823 26.956 18.709 1.00 0.00 C HETATM 45 N4 DNR A 2 23.988 28.200 19.036 1.00 0.00 N HETATM 46 C5 DNR A 2 24.553 26.398 17.647 1.00 0.00 C HETATM 47 C2' DNR A 2 22.362 22.986 16.052 1.00 0.00 C HETATM 48 C3' DNR A 2 22.612 21.534 15.691 1.00 0.00 C HETATM 49 O3' DNR A 2 21.598 20.691 16.194 1.00 0.00 O HETATM 50 H5' DNR A 2 24.817 20.922 14.489 1.00 0.00 H HETATM 51 H5'' DNR A 2 25.503 22.299 15.392 1.00 0.00 H HETATM 52 H4' DNR A 2 23.864 20.262 16.882 1.00 0.00 H HETATM 53 H1' DNR A 2 22.160 22.584 18.141 1.00 0.00 H HETATM 54 H6 DNR A 2 24.778 24.711 16.427 1.00 0.00 H HETATM 55 HN3 DNR A 2 22.306 26.678 20.054 1.00 0.00 H HETATM 56 H41 DNR A 2 23.457 28.587 19.831 1.00 0.00 H HETATM 57 H42 DNR A 2 24.572 28.775 18.430 1.00 0.00 H HETATM 58 H5 DNR A 2 25.335 26.946 17.146 1.00 0.00 H HETATM 59 H2' DNR A 2 22.945 23.619 15.386 1.00 0.00 H HETATM 60 H2'' DNR A 2 21.306 23.237 16.015 1.00 0.00 H HETATM 61 H3' DNR A 2 22.730 21.407 14.614 1.00 0.00 H