1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Padrta, P. Stefl, R. Zidek, L. Sklenar, V. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking NE J.Biomol.NMR JBNME9 0800 0925-2738 24 1 14 10.1023/A:1020632900961 12449414 Refinement of d(GCGAAGC) Hairpin Structure Using One- and Two-Bond Residual Dipolar Couplings 2002 10.2210/pdb1pqt/pdb pdb_00001pqt 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 2147.437 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' 1 syn polymer no no (DG)(DC)(DG)(DA)(DA)(DG)(DC) GCGAAGC A polydeoxyribonucleotide n n n n n n n -3.693 1 19 A 1 A 7 -0.092 A_DG1:DC7_A 1 5.939 -0.440 0.077 -0.215 16.068 1 19 A 2 A 6 -0.416 A_DC2:DG6_A 2 12.675 0.178 -0.255 -0.149 32.817 9 11 A 3 A 5 15.015 A_DG3:DA5_A 3 -2.319 6.211 1.254 -4.034 2.883 32.539 A A 1 2 10.410 A A 7 6 2.921 5.802 0.781 -0.126 AA_DG1DC2:DG6DC7_AA 1 1.326 -2.379 32.005 -1.132 -1.187 3.048 48.694 A A 2 3 13.079 A A 6 5 2.824 10.706 -0.106 1.380 AA_DC2DG3:DA5DG6_AA 2 0.319 -0.390 47.572 0.929 0.151 database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-07-01 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-03-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model 1KR8 is the same DNA hairpin but calculated with the simple parabolic potential as the penalty function for RDC restraints, unlike this entry where the flat-bottom potential was used for RDCs instead. RCSB Y RCSB 2003-06-19 REL REL THIS SEQUENCE OCCURS NATURALLY IN REPLICATION ORIGINS OF PHAGE PHIX174, IN HERPES SIMPLEX VIRUS, IN E. COLI HEAT-SHOCK GENE AND RRNA GENES. sample THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY IN ISOTROPIC AND LIQUID CRYSTALLINE PHASE. all calculated structures submitted 14 14 2D NOESY E-COSY DQF-COSY COUPLED HSQC S3E E-COSY 10 mM 6.7 1 atm 303 K molecular dynamics 7 6MM NATURAL ABUNDANCE D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, D2O; 6MM NATURAL ABUNDANCE D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, 90% H2O, 10% D2O; U-15N,13C, 0.5MM D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, 90% H2O, 10% D2O KOLLMAN, CASE ET. AL refinement Amber 7.0 Bruker collection XwinNMR 2.1 Bruker collection XwinNMR 3.0 T. D. Goddard and D. G. Kneller data analysis Sparky 3.X KOLLMAN, CASE ET. AL structure solution Amber 7.0 500 Bruker AVANCE G 1 n 1 DG 1 A C 2 n 2 DC 2 A G 3 n 3 DG 3 A A 4 n 4 DA 4 A A 5 n 5 DA 5 A G 6 n 6 DG 6 A C 7 n 7 DC 7 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A DA 4 0.085 SIDE CHAIN 1 A DA 5 0.057 SIDE CHAIN 1 A DG 6 0.065 SIDE CHAIN 2 A DA 4 0.085 SIDE CHAIN 2 A DA 5 0.069 SIDE CHAIN 3 A DA 4 0.086 SIDE CHAIN 3 A DA 5 0.064 SIDE CHAIN 4 A DA 4 0.083 SIDE CHAIN 4 A DA 5 0.064 SIDE CHAIN 5 A DA 4 0.086 SIDE CHAIN 5 A DA 5 0.059 SIDE CHAIN 5 A DG 6 0.057 SIDE CHAIN 6 A DA 4 0.080 SIDE CHAIN 6 A DA 5 0.072 SIDE CHAIN 7 A DA 4 0.082 SIDE CHAIN 7 A DA 5 0.073 SIDE CHAIN 8 A DA 4 0.074 SIDE CHAIN 8 A DA 5 0.062 SIDE CHAIN 9 A DA 4 0.082 SIDE CHAIN 9 A DA 5 0.070 SIDE CHAIN 10 A DA 4 0.088 SIDE CHAIN 10 A DA 5 0.076 SIDE CHAIN 11 A DA 4 0.083 SIDE CHAIN 11 A DA 5 0.068 SIDE CHAIN 12 A DA 4 0.079 SIDE CHAIN 12 A DA 5 0.059 SIDE CHAIN 12 A DG 6 0.060 SIDE CHAIN 13 A DA 4 0.084 SIDE CHAIN 13 A DA 5 0.072 SIDE CHAIN 14 A DA 4 0.082 SIDE CHAIN 14 A DA 5 0.071 SIDE CHAIN 1 1.82 0.30 108.30 110.12 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 2.44 0.30 108.30 110.74 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 3.30 0.50 117.70 121.00 A A A C5 C6 N1 DA DA DA 4 4 4 N 1 -4.58 0.60 118.60 114.02 A A A N1 C6 N6 DA DA DA 4 4 4 N 1 3.30 0.50 117.70 121.00 A A A C5 C6 N1 DA DA DA 5 5 5 N 1 -4.26 0.60 118.60 114.34 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 4.94 0.30 108.30 113.24 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 2.06 0.30 108.30 110.36 A A A O4' C1' N1 DC DC DC 7 7 7 N 2 2.54 0.30 108.30 110.84 A A A O4' C1' N9 DG DG DG 3 3 3 N 2 3.15 0.50 117.70 120.85 A A A C5 C6 N1 DA DA DA 4 4 4 N 2 -4.56 0.60 118.60 114.04 A A A N1 C6 N6 DA DA DA 4 4 4 N 2 3.28 0.50 117.70 120.98 A A A C5 C6 N1 DA DA DA 5 5 5 N 2 -4.26 0.60 118.60 114.34 A A A N1 C6 N6 DA DA DA 5 5 5 N 2 2.95 0.30 108.30 111.25 A A A O4' C1' N9 DG DG DG 6 6 6 N 3 1.89 0.30 108.30 110.19 A A A O4' C1' N9 DG DG DG 1 1 1 N 3 2.07 0.30 108.30 110.37 A A A O4' C1' N9 DG DG DG 3 3 3 N 3 3.34 0.50 117.70 121.04 A A A C5 C6 N1 DA DA DA 4 4 4 N 3 -4.44 0.60 118.60 114.16 A A A N1 C6 N6 DA DA DA 4 4 4 N 3 3.27 0.50 117.70 120.97 A A A C5 C6 N1 DA DA DA 5 5 5 N 3 -4.19 0.60 118.60 114.41 A A A N1 C6 N6 DA DA DA 5 5 5 N 3 3.77 0.30 108.30 112.07 A A A O4' C1' N9 DG DG DG 6 6 6 N 4 3.12 0.30 108.30 111.42 A A A O4' C1' N9 DG DG DG 3 3 3 N 4 3.25 0.50 117.70 120.95 A A A C5 C6 N1 DA DA DA 4 4 4 N 4 -4.44 0.60 118.60 114.16 A A A N1 C6 N6 DA DA DA 4 4 4 N 4 3.33 0.50 117.70 121.03 A A A C5 C6 N1 DA DA DA 5 5 5 N 4 -4.34 0.60 118.60 114.26 A A A N1 C6 N6 DA DA DA 5 5 5 N 4 3.36 0.30 108.30 111.66 A A A O4' C1' N9 DG DG DG 6 6 6 N 5 2.25 0.30 108.30 110.55 A A A O4' C1' N9 DG DG DG 3 3 3 N 5 3.25 0.50 117.70 120.95 A A A C5 C6 N1 DA DA DA 4 4 4 N 5 -4.65 0.60 118.60 113.95 A A A N1 C6 N6 DA DA DA 4 4 4 N 5 3.26 0.50 117.70 120.96 A A A C5 C6 N1 DA DA DA 5 5 5 N 5 -4.10 0.60 118.60 114.50 A A A N1 C6 N6 DA DA DA 5 5 5 N 5 4.31 0.30 108.30 112.61 A A A O4' C1' N9 DG DG DG 6 6 6 N 6 1.80 0.30 108.30 110.10 A A A O4' C1' N9 DG DG DG 1 1 1 N 6 2.19 0.30 108.30 110.49 A A A O4' C1' N9 DG DG DG 3 3 3 N 6 3.20 0.50 117.70 120.90 A A A C5 C6 N1 DA DA DA 4 4 4 N 6 -4.78 0.60 118.60 113.82 A A A N1 C6 N6 DA DA DA 4 4 4 N 6 3.17 0.50 117.70 120.87 A A A C5 C6 N1 DA DA DA 5 5 5 N 6 -4.19 0.60 118.60 114.41 A A A N1 C6 N6 DA DA DA 5 5 5 N 6 3.54 0.30 108.30 111.84 A A A O4' C1' N9 DG DG DG 6 6 6 N 7 2.09 0.30 108.30 110.39 A A A O4' C1' N9 DG DG DG 3 3 3 N 7 3.23 0.50 117.70 120.93 A A A C5 C6 N1 DA DA DA 4 4 4 N 7 -4.82 0.60 118.60 113.78 A A A N1 C6 N6 DA DA DA 4 4 4 N 7 3.26 0.50 117.70 120.96 A A A C5 C6 N1 DA DA DA 5 5 5 N 7 -4.31 0.60 118.60 114.29 A A A N1 C6 N6 DA DA DA 5 5 5 N 7 2.97 0.30 108.30 111.27 A A A O4' C1' N9 DG DG DG 6 6 6 N 8 1.85 0.30 108.30 110.15 A A A O4' C1' N9 DG DG DG 1 1 1 N 8 3.24 0.30 108.30 111.54 A A A O4' C1' N9 DG DG DG 3 3 3 N 8 3.26 0.50 117.70 120.96 A A A C5 C6 N1 DA DA DA 4 4 4 N 8 -4.68 0.60 118.60 113.92 A A A N1 C6 N6 DA DA DA 4 4 4 N 8 3.18 0.50 117.70 120.88 A A A C5 C6 N1 DA DA DA 5 5 5 N 8 -4.15 0.60 118.60 114.45 A A A N1 C6 N6 DA DA DA 5 5 5 N 8 2.95 0.30 108.30 111.25 A A A O4' C1' N9 DG DG DG 6 6 6 N 9 2.65 0.30 108.30 110.95 A A A O4' C1' N9 DG DG DG 3 3 3 N 9 3.15 0.50 117.70 120.85 A A A C5 C6 N1 DA DA DA 4 4 4 N 9 -4.46 0.60 118.60 114.14 A A A N1 C6 N6 DA DA DA 4 4 4 N 9 3.22 0.50 117.70 120.92 A A A C5 C6 N1 DA DA DA 5 5 5 N 9 -4.24 0.60 118.60 114.36 A A A N1 C6 N6 DA DA DA 5 5 5 N 9 3.52 0.30 108.30 111.82 A A A O4' C1' N9 DG DG DG 6 6 6 N 10 1.80 0.30 108.30 110.10 A A A O4' C1' N9 DG DG DG 1 1 1 N 10 3.17 0.50 117.70 120.87 A A A C5 C6 N1 DA DA DA 4 4 4 N 10 -4.48 0.60 118.60 114.12 A A A N1 C6 N6 DA DA DA 4 4 4 N 10 3.35 0.50 117.70 121.05 A A A C5 C6 N1 DA DA DA 5 5 5 N 10 -4.23 0.60 118.60 114.37 A A A N1 C6 N6 DA DA DA 5 5 5 N 10 3.58 0.30 108.30 111.88 A A A O4' C1' N9 DG DG DG 6 6 6 N 11 2.83 0.30 108.30 111.13 A A A O4' C1' N9 DG DG DG 3 3 3 N 11 3.27 0.50 117.70 120.97 A A A C5 C6 N1 DA DA DA 4 4 4 N 11 -4.46 0.60 118.60 114.14 A A A N1 C6 N6 DA DA DA 4 4 4 N 11 3.32 0.50 117.70 121.02 A A A C5 C6 N1 DA DA DA 5 5 5 N 11 -4.23 0.60 118.60 114.37 A A A N1 C6 N6 DA DA DA 5 5 5 N 11 2.84 0.30 108.30 111.14 A A A O4' C1' N9 DG DG DG 6 6 6 N 12 2.88 0.30 108.30 111.18 A A A O4' C1' N9 DG DG DG 1 1 1 N 12 2.05 0.30 108.30 110.35 A A A O4' C1' N9 DG DG DG 3 3 3 N 12 3.28 0.50 117.70 120.98 A A A C5 C6 N1 DA DA DA 4 4 4 N 12 -4.69 0.60 118.60 113.91 A A A N1 C6 N6 DA DA DA 4 4 4 N 12 3.36 0.50 117.70 121.06 A A A C5 C6 N1 DA DA DA 5 5 5 N 12 -4.33 0.60 118.60 114.27 A A A N1 C6 N6 DA DA DA 5 5 5 N 12 4.40 0.30 108.30 112.70 A A A O4' C1' N9 DG DG DG 6 6 6 N 12 1.90 0.30 108.30 110.20 A A A O4' C1' N1 DC DC DC 7 7 7 N 13 2.02 0.30 108.30 110.32 A A A O4' C1' N9 DG DG DG 1 1 1 N 13 2.18 0.30 108.30 110.48 A A A O4' C1' N9 DG DG DG 3 3 3 N 13 3.20 0.50 117.70 120.90 A A A C5 C6 N1 DA DA DA 4 4 4 N 13 -4.51 0.60 118.60 114.09 A A A N1 C6 N6 DA DA DA 4 4 4 N 13 3.25 0.50 117.70 120.95 A A A C5 C6 N1 DA DA DA 5 5 5 N 13 -4.25 0.60 118.60 114.35 A A A N1 C6 N6 DA DA DA 5 5 5 N 13 2.74 0.30 108.30 111.04 A A A O4' C1' N9 DG DG DG 6 6 6 N 14 1.82 0.30 108.30 110.12 A A A O4' C1' N9 DG DG DG 1 1 1 N 14 2.41 0.30 108.30 110.71 A A A O4' C1' N9 DG DG DG 3 3 3 N 14 3.26 0.50 117.70 120.96 A A A C5 C6 N1 DA DA DA 4 4 4 N 14 -4.47 0.60 118.60 114.13 A A A N1 C6 N6 DA DA DA 4 4 4 N 14 3.32 0.50 117.70 121.02 A A A C5 C6 N1 DA DA DA 5 5 5 N 14 -4.30 0.60 118.60 114.30 A A A N1 C6 N6 DA DA DA 5 5 5 N 14 3.29 0.30 108.30 111.59 A A A O4' C1' N9 DG DG DG 6 6 6 N REFINEMENT OF d(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TWO-BOND RESIDUAL DIPOLAR COUPLINGS 1 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 7 A N3 DC 7 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 7 A O2 DC 7 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 7 A N4 DC 7 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 6 A N1 DG 6 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 6 A O6 DG 6 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 6 A N2 DG 6 1_555 hydrog TYPE_11_PAIR A DG 3 A N2 DG 3 1_555 A DA 5 A N7 DA 5 1_555 hydrog TYPE_11_PAIR A DG 3 A N3 DG 3 1_555 A DA 5 A N6 DA 5 1_555 DNA HAIRPIN, DNA, GA MISMATCH 1PQT PDB 1 1PQT 1 7 1PQT 1 7 1PQT A 1 1 7 1 P 1