HEADER DNA 12-DEC-23 8XEQ TITLE SOLUTION NMR STRUCTURE OF DNA SEQUENCE D(CGATCG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*CP*GP*TP*GP*)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS ONCOGENE, GENE REGULATION, DUPLEX B FORM, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR M.S.NAIR,S.KUMAR REVDAT 2 15-MAY-24 8XEQ 1 REMARK REVDAT 1 10-JAN-24 8XEQ 0 JRNL AUTH M.S.NAIR,S.KUMAR JRNL TITL SOLUTION NMR STRUCTURE OF DNA SEQUENCE D(CGATCG)2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 18 REMARK 3 AUTHORS : D.A. CASE, I.Y. BEN-SHALOM, S.R. BROZELL, D.S. REMARK 3 CERUTTI, T.E. CHEATHAM, III, V.W.D. CRUZEIRO, T.A. REMARK 3 DARDEN, R.E. DUKE, D. GHOREISHI, M.K. GILSON, H. REMARK 3 GOHLKE, A.W. GOETZ, D. GREENE, R HARRIS, N. REMARK 3 HOMEYER, Y. HUANG, S. IZADI, A. KOVALENKO, T. REMARK 3 KURTZMAN, T.S. LEE, S. LEGRAND, P. LI, C. LIN, J. REMARK 3 LIU, T. LUCHKO, R. LUO, D.J. MERMELSTEIN, K.M. REMARK 3 MERZ, Y. MIAO, G. MONARD, C. NGUYEN, H. NGUYEN, I. REMARK 3 OMELYAN, A. ONUFRIEV, F. PAN, R. QI, D.R. ROE, A. REMARK 3 ROITBERG, C. SAGUI, S. SCHOTT-VERDUGO, J. SHEN, REMARK 3 C.L. SIMMERLING, J. SMITH, R. SALOMONFERRER, J. REMARK 3 SWAILS, R.C. WALKER, J. WANG, H. WEI, R.M. WOLF, REMARK 3 X. WU, L. XIAO, D.M. YORK AND P.A. KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 171 NOE DERIVED REMARK 3 DISTSNCE RESTRAINTS. REMARK 4 REMARK 4 8XEQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300042964. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.56 W/V HEXAMER DNA, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, TOPSPIN 4.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 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 DA A 2 C5' DA A 2 C4' 0.047 REMARK 500 1 DA A 2 C5 DA A 2 C6 -0.055 REMARK 500 1 DG A 4 N3 DG A 4 C4 0.058 REMARK 500 1 DG A 4 C6 DG A 4 N1 -0.043 REMARK 500 1 DT A 5 C2' DT A 5 C1' 0.078 REMARK 500 1 DG A 6 P DG A 6 O5' 0.070 REMARK 500 1 DG A 6 N1 DG A 6 C2 -0.071 REMARK 500 1 DG A 6 N9 DG A 6 C4 -0.051 REMARK 500 1 DC B 7 O4' DC B 7 C4' -0.077 REMARK 500 1 DC B 7 N1 DC B 7 C6 -0.037 REMARK 500 1 DA B 8 N9 DA B 8 C4 0.043 REMARK 500 1 DC B 9 O4' DC B 9 C4' -0.080 REMARK 500 1 DC B 9 O3' DG B 10 P -0.113 REMARK 500 1 DG B 10 C5' DG B 10 C4' 0.053 REMARK 500 1 DG B 10 C5 DG B 10 N7 0.046 REMARK 500 1 DG B 10 N9 DG B 10 C4 0.048 REMARK 500 1 DG B 10 C2 DG B 10 N2 -0.079 REMARK 500 1 DT B 11 N1 DT B 11 C2 0.108 REMARK 500 1 DT B 11 C5 DT B 11 C6 0.043 REMARK 500 1 DT B 11 C5 DT B 11 C7 0.049 REMARK 500 1 DT B 11 O3' DG B 12 P -0.090 REMARK 500 1 DG B 12 N7 DG B 12 C8 0.044 REMARK 500 1 DG B 12 C2 DG B 12 N2 -0.060 REMARK 500 2 DC A 1 C3' DC A 1 C2' -0.056 REMARK 500 2 DC A 1 C2' DC A 1 C1' 0.063 REMARK 500 2 DC A 1 C4 DC A 1 N4 -0.069 REMARK 500 2 DC A 1 N3 DC A 1 C4 -0.058 REMARK 500 2 DC A 1 C5 DC A 1 C6 0.050 REMARK 500 2 DA A 2 C4' DA A 2 C3' -0.066 REMARK 500 2 DA A 2 N3 DA A 2 C4 0.081 REMARK 500 2 DA A 2 C6 DA A 2 N1 -0.063 REMARK 500 2 DC A 3 O4' DC A 3 C4' -0.065 REMARK 500 2 DC A 3 N1 DC A 3 C2 0.078 REMARK 500 2 DC A 3 C5 DC A 3 C6 0.056 REMARK 500 2 DG A 4 C5' DG A 4 C4' 0.047 REMARK 500 2 DG A 4 C2 DG A 4 N3 0.070 REMARK 500 2 DG A 4 C2 DG A 4 N2 -0.071 REMARK 500 2 DT A 5 C5' DT A 5 C4' 0.081 REMARK 500 2 DC B 7 O4' DC B 7 C4' -0.061 REMARK 500 2 DA B 8 C2' DA B 8 C1' -0.065 REMARK 500 2 DC B 9 C4 DC B 9 N4 -0.054 REMARK 500 2 DC B 9 C4 DC B 9 C5 -0.062 REMARK 500 2 DG B 10 C5 DG B 10 N7 0.058 REMARK 500 2 DT B 11 C5 DT B 11 C7 0.050 REMARK 500 2 DG B 12 C2 DG B 12 N2 -0.067 REMARK 500 3 DC A 1 O3' DA A 2 P -0.082 REMARK 500 3 DA A 2 P DA A 2 O5' 0.110 REMARK 500 3 DA A 2 C5' DA A 2 C4' 0.048 REMARK 500 3 DC A 3 C5' DC A 3 C4' 0.057 REMARK 500 3 DG A 4 O4' DG A 4 C4' -0.080 REMARK 500 REMARK 500 THIS ENTRY HAS 197 BOND DEVIATIONS. 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 DC A 1 C2 - N3 - C4 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DC A 1 N3 - C4 - C5 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 1 C4 - C5 - C6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DC A 1 N3 - C4 - N4 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA A 2 N1 - C6 - N6 ANGL. DEV. = -10.1 DEGREES REMARK 500 1 DA A 2 C5 - C6 - N6 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DC A 3 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DC A 3 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DC A 3 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 4 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 4 O4' - C1' - C2' ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 4 N3 - C4 - C5 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 4 N1 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 5 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 5 C2 - N3 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT A 5 C5 - C4 - O4 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG A 6 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 6 N3 - C4 - C5 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DC B 7 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DC B 7 C2 - N3 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DC B 7 N1 - C2 - O2 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DC B 7 N3 - C2 - O2 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DC B 7 N3 - C4 - N4 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DC B 7 C5 - C4 - N4 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA B 8 C5' - C4' - O4' ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC B 9 C6 - N1 - C2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC B 9 N1 - C2 - N3 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC B 9 C2 - N3 - C4 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC B 9 N3 - C2 - O2 ANGL. DEV. = -8.3 DEGREES REMARK 500 1 DC B 9 N3 - C4 - N4 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DC B 9 C5 - C4 - N4 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DC B 9 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 10 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG B 10 N3 - C4 - C5 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT B 11 O4' - C4' - C3' ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT B 11 C4' - C3' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DT B 11 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DT B 11 N1 - C2 - N3 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT B 11 N1 - C2 - O2 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT B 11 C4 - C5 - C7 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT B 11 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 12 N3 - C4 - C5 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 501 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 DA A 2 0.11 SIDE CHAIN REMARK 500 1 DC A 3 0.10 SIDE CHAIN REMARK 500 1 DG A 4 0.06 SIDE CHAIN REMARK 500 1 DT A 5 0.10 SIDE CHAIN REMARK 500 1 DG A 6 0.09 SIDE CHAIN REMARK 500 1 DC B 7 0.09 SIDE CHAIN REMARK 500 1 DA B 8 0.15 SIDE CHAIN REMARK 500 1 DC B 9 0.15 SIDE CHAIN REMARK 500 1 DT B 11 0.06 SIDE CHAIN REMARK 500 1 DG B 12 0.07 SIDE CHAIN REMARK 500 2 DA A 2 0.07 SIDE CHAIN REMARK 500 2 DC A 3 0.09 SIDE CHAIN REMARK 500 2 DT A 5 0.07 SIDE CHAIN REMARK 500 2 DG A 6 0.12 SIDE CHAIN REMARK 500 2 DA B 8 0.11 SIDE CHAIN REMARK 500 2 DC B 9 0.08 SIDE CHAIN REMARK 500 2 DG B 10 0.06 SIDE CHAIN REMARK 500 3 DA A 2 0.09 SIDE CHAIN REMARK 500 3 DT A 5 0.13 SIDE CHAIN REMARK 500 3 DG A 6 0.09 SIDE CHAIN REMARK 500 3 DC B 7 0.07 SIDE CHAIN REMARK 500 3 DA B 8 0.07 SIDE CHAIN REMARK 500 3 DC B 9 0.07 SIDE CHAIN REMARK 500 3 DG B 10 0.06 SIDE CHAIN REMARK 500 3 DT B 11 0.10 SIDE CHAIN REMARK 500 4 DC A 1 0.12 SIDE CHAIN REMARK 500 4 DA A 2 0.12 SIDE CHAIN REMARK 500 4 DC A 3 0.09 SIDE CHAIN REMARK 500 4 DG A 4 0.06 SIDE CHAIN REMARK 500 4 DA B 8 0.10 SIDE CHAIN REMARK 500 4 DC B 9 0.12 SIDE CHAIN REMARK 500 4 DG B 10 0.07 SIDE CHAIN REMARK 500 4 DG B 12 0.10 SIDE CHAIN REMARK 500 5 DA A 2 0.09 SIDE CHAIN REMARK 500 5 DC A 3 0.08 SIDE CHAIN REMARK 500 5 DT A 5 0.08 SIDE CHAIN REMARK 500 5 DG A 6 0.08 SIDE CHAIN REMARK 500 5 DA B 8 0.09 SIDE CHAIN REMARK 500 5 DC B 9 0.10 SIDE CHAIN REMARK 500 5 DT B 11 0.09 SIDE CHAIN REMARK 500 5 DG B 12 0.10 SIDE CHAIN REMARK 500 6 DA A 2 0.10 SIDE CHAIN REMARK 500 6 DC A 3 0.13 SIDE CHAIN REMARK 500 6 DT A 5 0.08 SIDE CHAIN REMARK 500 6 DC B 7 0.09 SIDE CHAIN REMARK 500 6 DA B 8 0.06 SIDE CHAIN REMARK 500 6 DC B 9 0.09 SIDE CHAIN REMARK 500 6 DT B 11 0.08 SIDE CHAIN REMARK 500 6 DG B 12 0.07 SIDE CHAIN REMARK 500 7 DC A 1 0.13 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 64 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36623 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF DNA SEQUENCE D(CGATCG)2 DBREF 8XEQ A 1 6 PDB 8XEQ 8XEQ 1 6 DBREF 8XEQ B 7 12 PDB 8XEQ 8XEQ 7 12 SEQRES 1 A 6 DC DA DC DG DT DG SEQRES 1 B 6 DC DA DC DG DT DG CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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