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 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/pdb1kr8/pdb pdb_00001kr8 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 -0.889 1 19 A 1 A 7 -0.034 A_DG1:DC7_A 1 1.387 -0.482 0.046 -0.217 18.787 1 19 A 2 A 6 -0.099 A_DC2:DG6_A 2 3.148 0.258 -0.121 -0.153 36.932 9 11 A 3 A 5 18.265 A_DG3:DA5_A 3 -2.720 6.097 1.475 -4.033 2.774 29.402 A A 1 2 9.135 A A 7 6 2.873 4.618 0.448 -0.368 AA_DG1DC2:DG6DC7_AA 1 -0.526 1.040 29.040 -1.584 -0.980 3.111 52.148 A A 2 3 12.747 A A 6 5 2.945 11.124 -0.199 1.100 AA_DC2DG3:DA5DG6_AA 2 -3.274 3.752 50.930 0.558 0.023 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 2002-12-11 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model RCSB Y RCSB 2002-01-09 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 2D NOESY E-COSY DQF-COSY coupled HSQC S3E E-COSY 10 mM 6.7 1 atm 303 K 10 mM 6.7 1 atm 277 K 10 mM 6.7 1 atm 303 K molecular dynamics 7 closest to the average 6mM natural abundance d(GCGAAGC), 10mM phosphate buffer Na, D2O D2O 6mM natural abundance d(GCGAAGC), 10mM phosphate buffer Na, 90% H2O, 10% D2O 90% H2O/10% D2O U-15N,13C, 0.5mM d(GCGAAGC), 10mM phosphate buffer Na, 90% H2O, 10% D2O 90% H2O/10% D2O Bruker collection XwinNMR 2.1, 3.0 Bruker processing XwinNMR 2.1, 3.0 T. D. Goddard and D. G. Kneller data analysis Sparky 3.x Kollman, Case et. al structure solution Amber 6.0 Kollman, Case et. al refinement Amber 6.0 500 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 0.083 SIDE CHAIN 1 A DA 5 0.081 SIDE CHAIN 2 A DG 3 0.061 SIDE CHAIN 2 A DA 4 0.062 SIDE CHAIN 2 A DA 5 0.100 SIDE CHAIN 2 A DG 6 0.065 SIDE CHAIN 3 A DG 3 0.061 SIDE CHAIN 3 A DA 4 0.078 SIDE CHAIN 3 A DA 5 0.084 SIDE CHAIN 4 A DG 3 0.064 SIDE CHAIN 4 A DA 4 0.062 SIDE CHAIN 4 A DA 5 0.103 SIDE CHAIN 4 A DG 6 0.070 SIDE CHAIN 5 A DA 5 0.096 SIDE CHAIN 5 A DG 6 0.071 SIDE CHAIN 6 A DA 4 0.068 SIDE CHAIN 6 A DA 5 0.083 SIDE CHAIN 7 A DG 3 0.065 SIDE CHAIN 7 A DA 5 0.090 SIDE CHAIN 8 A DG 3 0.064 SIDE CHAIN 8 A DA 4 0.069 SIDE CHAIN 8 A DA 5 0.087 SIDE CHAIN 9 A DA 5 0.090 SIDE CHAIN 9 A DG 6 0.057 SIDE CHAIN 10 A DG 3 0.065 SIDE CHAIN 10 A DA 4 0.059 SIDE CHAIN 10 A DA 5 0.097 SIDE CHAIN 11 A DG 3 0.077 SIDE CHAIN 11 A DA 5 0.113 SIDE CHAIN 11 A DG 6 0.099 SIDE CHAIN 12 A DG 3 0.058 SIDE CHAIN 12 A DA 5 0.096 SIDE CHAIN 13 A DG 3 0.049 SIDE CHAIN 13 A DA 5 0.105 SIDE CHAIN 13 A DG 6 0.081 SIDE CHAIN 14 A DA 4 0.083 SIDE CHAIN 14 A DA 5 0.078 SIDE CHAIN 1 2.79 0.30 108.30 111.09 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 -6.01 0.80 105.90 99.89 A A A O4' C1' C2' DC DC DC 2 2 2 N 1 3.28 0.50 117.70 120.98 A A A C5 C6 N1 DA DA DA 4 4 4 N 1 -4.07 0.60 118.60 114.53 A A A N1 C6 N6 DA DA DA 4 4 4 N 1 -11.94 1.90 104.00 92.06 A A A O3' P O5' DA DA DA 4 5 5 Y 1 3.34 0.50 117.70 121.04 A A A C5 C6 N1 DA DA DA 5 5 5 N 1 -4.33 0.60 118.60 114.27 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 4.68 0.30 108.30 112.98 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -2.41 0.40 106.40 103.99 A A A C8 N9 C4 DG DG DG 6 6 6 N 1 2.08 0.30 108.30 110.38 A A A O4' C1' N1 DC DC DC 7 7 7 N 2 2.03 0.30 108.30 110.33 A A A O4' C1' N9 DG DG DG 1 1 1 N 2 -5.75 0.80 105.90 100.15 A A A O4' C1' C2' DC DC DC 2 2 2 N 2 3.17 0.50 117.70 120.87 A A A C5 C6 N1 DA DA DA 4 4 4 N 2 -4.07 0.60 118.60 114.53 A A A N1 C6 N6 DA DA DA 4 4 4 N 2 3.29 0.50 117.70 120.99 A A A C5 C6 N1 DA DA DA 5 5 5 N 2 -4.21 0.60 118.60 114.39 A A A N1 C6 N6 DA DA DA 5 5 5 N 2 3.67 0.30 108.30 111.97 A A A O4' C1' N9 DG DG DG 6 6 6 N 2 -2.49 0.40 106.40 103.91 A A A C8 N9 C4 DG DG DG 6 6 6 N 3 2.13 0.30 108.30 110.43 A A A O4' C1' N9 DG DG DG 1 1 1 N 3 -6.02 0.80 105.90 99.88 A A A O4' C1' C2' DC DC DC 2 2 2 N 3 3.36 0.50 117.70 121.06 A A A C5 C6 N1 DA DA DA 4 4 4 N 3 -4.22 0.60 118.60 114.38 A A A N1 C6 N6 DA DA DA 4 4 4 N 3 -12.13 1.90 104.00 91.87 A A A O3' P O5' DA DA DA 4 5 5 Y 3 3.34 0.50 117.70 121.04 A A A C5 C6 N1 DA DA DA 5 5 5 N 3 -4.60 0.60 118.60 114.00 A A A N1 C6 N6 DA DA DA 5 5 5 N 3 3.92 0.30 108.30 112.22 A A A O4' C1' N9 DG DG DG 6 6 6 N 3 -2.53 0.40 106.40 103.87 A A A C8 N9 C4 DG DG DG 6 6 6 N 4 2.37 0.30 108.30 110.67 A A A O4' C1' N9 DG DG DG 1 1 1 N 4 -5.61 0.80 105.90 100.29 A A A O4' C1' C2' DC DC DC 2 2 2 N 4 3.36 0.50 117.70 121.06 A A A C5 C6 N1 DA DA DA 4 4 4 N 4 -4.22 0.60 118.60 114.38 A A A N1 C6 N6 DA DA DA 4 4 4 N 4 -3.16 0.50 117.00 113.84 A A A C4 C5 C6 DA DA DA 5 5 5 N 4 3.52 0.50 117.70 121.22 A A A C5 C6 N1 DA DA DA 5 5 5 N 4 -4.45 0.60 118.60 114.15 A A A N1 C6 N6 DA DA DA 5 5 5 N 4 2.88 0.30 108.30 111.18 A A A O4' C1' N9 DG DG DG 6 6 6 N 4 -2.47 0.40 106.40 103.93 A A A C8 N9 C4 DG DG DG 6 6 6 N 5 2.17 0.30 108.30 110.47 A A A O4' C1' N9 DG DG DG 1 1 1 N 5 -5.78 0.80 105.90 100.12 A A A O4' C1' C2' DC DC DC 2 2 2 N 5 3.13 0.50 117.70 120.83 A A A C5 C6 N1 DA DA DA 4 4 4 N 5 -4.18 0.60 118.60 114.42 A A A N1 C6 N6 DA DA DA 4 4 4 N 5 -13.22 1.90 104.00 90.78 A A A O3' P O5' DA DA DA 4 5 5 Y 5 3.31 0.50 117.70 121.01 A A A C5 C6 N1 DA DA DA 5 5 5 N 5 -4.31 0.60 118.60 114.29 A A A N1 C6 N6 DA DA DA 5 5 5 N 5 2.08 0.30 108.30 110.38 A A A O4' C1' N9 DG DG DG 6 6 6 N 5 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 DG DG DG 6 6 6 N 5 -5.29 0.70 108.00 102.71 A A A O4' C1' N1 DC DC DC 7 7 7 N 6 2.77 0.30 108.30 111.07 A A A O4' C1' N9 DG DG DG 1 1 1 N 6 -5.93 0.80 105.90 99.97 A A A O4' C1' C2' DC DC DC 2 2 2 N 6 3.30 0.50 117.70 121.00 A A A C5 C6 N1 DA DA DA 4 4 4 N 6 -4.28 0.60 118.60 114.32 A A A N1 C6 N6 DA DA DA 4 4 4 N 6 -12.54 1.90 104.00 91.46 A A A O3' P O5' DA DA DA 4 5 5 Y 6 3.30 0.50 117.70 121.00 A A A C5 C6 N1 DA DA DA 5 5 5 N 6 -4.37 0.60 118.60 114.23 A A A N1 C6 N6 DA DA DA 5 5 5 N 6 3.45 0.30 108.30 111.75 A A A O4' C1' N9 DG DG DG 6 6 6 N 7 -6.10 0.80 105.90 99.80 A A A O4' C1' C2' DC DC DC 2 2 2 N 7 -4.26 0.70 121.90 117.64 A A A N3 C2 O2 DC DC DC 2 2 2 N 7 3.22 0.50 117.70 120.92 A A A C5 C6 N1 DA DA DA 4 4 4 N 7 -4.33 0.60 118.60 114.27 A A A N1 C6 N6 DA DA DA 4 4 4 N 7 -12.82 1.90 104.00 91.18 A A A O3' P O5' DA DA DA 4 5 5 Y 7 -3.09 0.50 117.00 113.91 A A A C4 C5 C6 DA DA DA 5 5 5 N 7 3.48 0.50 117.70 121.18 A A A C5 C6 N1 DA DA DA 5 5 5 N 7 -4.57 0.60 118.60 114.03 A A A N1 C6 N6 DA DA DA 5 5 5 N 7 2.66 0.30 108.30 110.96 A A A O4' C1' N9 DG DG DG 6 6 6 N 7 -2.91 0.40 106.40 103.49 A A A C8 N9 C4 DG DG DG 6 6 6 N 8 1.95 0.30 108.30 110.25 A A A O4' C1' N9 DG DG DG 1 1 1 N 8 -5.98 0.80 105.90 99.92 A A A O4' C1' C2' DC DC DC 2 2 2 N 8 3.28 0.50 117.70 120.98 A A A C5 C6 N1 DA DA DA 4 4 4 N 8 -4.12 0.60 118.60 114.48 A A A N1 C6 N6 DA DA DA 4 4 4 N 8 -11.87 1.90 104.00 92.13 A A A O3' P O5' DA DA DA 4 5 5 Y 8 -3.03 0.50 117.00 113.97 A A A C4 C5 C6 DA DA DA 5 5 5 N 8 3.49 0.50 117.70 121.19 A A A C5 C6 N1 DA DA DA 5 5 5 N 8 -4.37 0.60 118.60 114.23 A A A N1 C6 N6 DA DA DA 5 5 5 N 8 2.83 0.30 108.30 111.13 A A A O4' C1' N9 DG DG DG 6 6 6 N 8 -2.51 0.40 106.40 103.89 A A A C8 N9 C4 DG DG DG 6 6 6 N 9 1.88 0.30 108.30 110.18 A A A O4' C1' N9 DG DG DG 1 1 1 N 9 -5.88 0.80 105.90 100.02 A A A O4' C1' C2' DC DC DC 2 2 2 N 9 3.13 0.50 117.70 120.83 A A A C5 C6 N1 DA DA DA 4 4 4 N 9 -4.09 0.60 118.60 114.51 A A A N1 C6 N6 DA DA DA 4 4 4 N 9 -13.04 1.90 104.00 90.96 A A A O3' P O5' DA DA DA 4 5 5 Y 9 3.26 0.50 117.70 120.96 A A A C5 C6 N1 DA DA DA 5 5 5 N 9 -4.31 0.60 118.60 114.29 A A A N1 C6 N6 DA DA DA 5 5 5 N 9 3.87 0.30 108.30 112.17 A A A O4' C1' N9 DG DG DG 6 6 6 N 9 -2.58 0.40 106.40 103.82 A A A C8 N9 C4 DG DG DG 6 6 6 N 10 2.19 0.30 108.30 110.49 A A A O4' C1' N9 DG DG DG 1 1 1 N 10 -5.83 0.80 105.90 100.07 A A A O4' C1' C2' DC DC DC 2 2 2 N 10 3.09 0.50 117.70 120.79 A A A C5 C6 N1 DA DA DA 4 4 4 N 10 -3.94 0.60 118.60 114.66 A A A N1 C6 N6 DA DA DA 4 4 4 N 10 -11.83 1.90 104.00 92.17 A A A O3' P O5' DA DA DA 4 5 5 Y 10 3.34 0.50 117.70 121.04 A A A C5 C6 N1 DA DA DA 5 5 5 N 10 -4.47 0.60 118.60 114.13 A A A N1 C6 N6 DA DA DA 5 5 5 N 10 3.95 0.30 108.30 112.25 A A A O4' C1' N9 DG DG DG 6 6 6 N 10 -2.86 0.40 106.40 103.54 A A A C8 N9 C4 DG DG DG 6 6 6 N 11 -5.69 0.80 105.90 100.21 A A A O4' C1' C2' DC DC DC 2 2 2 N 11 3.07 0.50 117.70 120.77 A A A C5 C6 N1 DA DA DA 4 4 4 N 11 -4.11 0.60 118.60 114.49 A A A N1 C6 N6 DA DA DA 4 4 4 N 11 -3.19 0.50 117.00 113.81 A A A C4 C5 C6 DA DA DA 5 5 5 N 11 3.52 0.50 117.70 121.22 A A A C5 C6 N1 DA DA DA 5 5 5 N 11 -4.42 0.60 118.60 114.18 A A A N1 C6 N6 DA DA DA 5 5 5 N 11 3.74 0.30 108.30 112.04 A A A O4' C1' N9 DG DG DG 6 6 6 N 11 -2.84 0.40 106.40 103.56 A A A C8 N9 C4 DG DG DG 6 6 6 N 12 2.28 0.30 108.30 110.58 A A A O4' C1' N9 DG DG DG 1 1 1 N 12 -5.91 0.80 105.90 99.99 A A A O4' C1' C2' DC DC DC 2 2 2 N 12 3.18 0.50 117.70 120.88 A A A C5 C6 N1 DA DA DA 4 4 4 N 12 -4.11 0.60 118.60 114.49 A A A N1 C6 N6 DA DA DA 4 4 4 N 12 -12.03 1.90 104.00 91.97 A A A O3' P O5' DA DA DA 4 5 5 Y 12 3.32 0.50 117.70 121.02 A A A C5 C6 N1 DA DA DA 5 5 5 N 12 -4.36 0.60 118.60 114.24 A A A N1 C6 N6 DA DA DA 5 5 5 N 12 3.62 0.30 108.30 111.92 A A A O4' C1' N9 DG DG DG 6 6 6 N 12 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 DG DG DG 6 6 6 N 12 9.07 1.40 114.30 123.37 A A A N1 C1' C2' DC DC DC 7 7 7 N 12 -5.60 0.70 108.00 102.40 A A A O4' C1' N1 DC DC DC 7 7 7 N 13 2.04 0.30 108.30 110.34 A A A O4' C1' N9 DG DG DG 1 1 1 N 13 -5.73 0.80 105.90 100.17 A A A O4' C1' C2' DC DC DC 2 2 2 N 13 3.10 0.50 117.70 120.80 A A A C5 C6 N1 DA DA DA 4 4 4 N 13 -3.92 0.60 118.60 114.68 A A A N1 C6 N6 DA DA DA 4 4 4 N 13 -11.56 1.90 104.00 92.44 A A A O3' P O5' DA DA DA 4 5 5 Y 13 -3.14 0.50 117.00 113.86 A A A C4 C5 C6 DA DA DA 5 5 5 N 13 3.48 0.50 117.70 121.18 A A A C5 C6 N1 DA DA DA 5 5 5 N 13 -4.42 0.60 118.60 114.18 A A A N1 C6 N6 DA DA DA 5 5 5 N 13 4.02 0.30 108.30 112.32 A A A O4' C1' N9 DG DG DG 6 6 6 N 13 -2.73 0.40 106.40 103.67 A A A C8 N9 C4 DG DG DG 6 6 6 N 14 2.26 0.30 108.30 110.56 A A A O4' C1' N9 DG DG DG 1 1 1 N 14 -5.90 0.80 105.90 100.00 A A A O4' C1' C2' DC DC DC 2 2 2 N 14 3.32 0.50 117.70 121.02 A A A C5 C6 N1 DA DA DA 4 4 4 N 14 -4.18 0.60 118.60 114.42 A A A N1 C6 N6 DA DA DA 4 4 4 N 14 -12.15 1.90 104.00 91.85 A A A O3' P O5' DA DA DA 4 5 5 Y 14 3.42 0.50 117.70 121.12 A A A C5 C6 N1 DA DA DA 5 5 5 N 14 -4.52 0.60 118.60 114.08 A A A N1 C6 N6 DA DA DA 5 5 5 N 14 3.90 0.30 108.30 112.20 A A A O4' C1' N9 DG DG DG 6 6 6 N 14 -2.60 0.40 106.40 103.80 A A A C8 N9 C4 DG DG DG 6 6 6 N Refinement of d(GCGAAGC) Hairpin Structure Using One-and Two-Bonds 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 1KR8 PDB 1 1KR8 1 7 1KR8 1 7 1KR8 A 1 1 7