1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Clore, G.M. Kuszewski, J. 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 C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing US J.Am.Chem.Soc. JACSAT 0004 0002-7863 123 3903 3918 10.1021/ja010033u 11457140 Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions. 2001 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 122 6190 6200 10.1021/ja000324n The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase 2000 10.2210/pdb1gip/pdb pdb_00001gip 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3663.392 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' 2 syn polymer no no (DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n -1.425 1 19 A 1 B 24 0.224 A_DC1:DG24_B 1 -16.655 0.088 -0.059 -0.195 1.742 1 19 A 2 B 23 0.374 A_DG2:DC23_B 2 -11.590 -0.124 0.187 -0.172 -2.837 1 19 A 3 B 22 -1.866 A_DC3:DG22_B 3 -10.192 0.093 0.107 -0.164 3.882 1 19 A 4 B 21 -0.102 A_DG4:DC21_B 4 -10.441 -0.114 0.032 -0.178 0.519 1 20 A 5 B 20 2.414 A_DA5:DT20_B 5 -18.943 -0.027 -0.200 -0.125 1.840 1 20 A 6 B 19 2.064 A_DA6:DT19_B 6 -22.050 -0.021 -0.162 -0.136 -1.852 1 20 A 7 B 18 2.062 A_DT7:DA18_B 7 -22.052 0.022 -0.162 -0.136 -0.487 1 20 A 8 B 17 2.426 A_DT8:DA17_B 8 -18.942 0.028 -0.202 -0.126 -3.885 1 19 A 9 B 16 -0.090 A_DC9:DG16_B 9 -10.461 0.113 0.032 -0.178 2.809 1 19 A 10 B 15 -1.858 A_DG10:DC15_B 10 -10.169 -0.093 0.106 -0.164 -1.731 1 19 A 11 B 14 0.379 A_DC11:DG14_B 11 -11.575 0.125 0.185 -0.172 1.434 1 19 A 12 B 13 0.219 A_DG12:DC13_B 12 -16.675 -0.087 -0.061 -0.196 3.443 37.832 A A 1 2 14.673 B B 24 23 3.475 9.414 -0.281 0.244 AA_DC1DG2:DC23DG24_BB 1 -2.561 3.991 36.597 -0.927 0.079 3.609 33.693 A A 2 3 -2.792 B B 23 22 3.588 -1.618 -0.203 -0.622 AA_DG2DC3:DG22DC23_BB 2 0.621 -1.071 33.650 -0.784 0.461 3.396 34.808 A A 3 4 17.699 B B 22 21 3.435 10.435 -0.129 0.383 AA_DC3DG4:DC21DG22_BB 3 0.190 -0.322 33.253 -1.059 0.247 3.387 34.426 A A 4 5 10.457 B B 21 20 3.458 6.157 -0.147 -0.116 AA_DG4DA5:DT20DC21_BB 4 -0.359 0.609 33.886 -1.207 0.190 3.355 37.374 A A 5 6 1.757 B B 20 19 3.349 1.125 -0.231 0.008 AA_DA5DA6:DT19DT20_BB 5 -1.773 2.769 37.317 -0.139 0.120 3.381 37.005 A A 6 7 -6.340 B B 19 18 3.361 -4.016 -0.001 -0.363 AA_DA6DT7:DA18DT19_BB 6 -0.007 0.011 36.794 -0.014 0.000 3.354 37.371 A A 7 8 1.745 B B 18 17 3.348 1.117 0.231 0.009 AA_DT7DT8:DA17DA18_BB 7 1.788 -2.792 37.314 -0.137 -0.118 3.388 34.430 A A 8 9 10.483 B B 17 16 3.459 6.173 0.147 -0.116 AA_DT8DC9:DG16DA17_BB 8 0.346 -0.587 33.886 -1.210 -0.192 3.398 34.798 A A 9 10 17.661 B B 16 15 3.435 10.410 0.130 0.384 AA_DC9DG10:DC15DG16_BB 9 -0.190 0.322 33.250 -1.055 -0.248 3.608 33.701 A A 10 11 -2.769 B B 15 14 3.587 -1.605 0.203 -0.622 AA_DG10DC11:DG14DC15_BB 10 -0.609 1.051 33.658 -0.786 -0.459 3.442 37.831 A A 11 12 14.697 B B 14 13 3.475 9.429 0.281 0.243 AA_DC11DG12:DC13DG14_BB 11 2.564 -3.996 36.593 -0.929 -0.079 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Data collection 1 0 2001-08-01 1 1 2008-04-26 1 2 2011-07-13 1 3 2022-02-23 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name DREW AND DICKERSON DODECAMER HIGH RESOLUTION DREW AND DICKERSON DODECAMER DODECAMER DETERMINED FROM DIPOLAR COUPLINGS RCSB Y RCSB 2001-02-20 REL THE NUMBER OF CALCULATED CONFORMERS IS 20 WITH NOES AND DIPOLAR COUPLINGS AND 20 WITH DIPOLAR COUPLINGS ONLY THE RESTRAINED REGULARIZED MEAN STRUCTURES 40 2 13C-HSQC-J-MODULATED COSY 13C-HSQC-F1- COUPLED 15N-HSQC-F1- COUPLED 2D NOESY 40 mM 7.00 1 atm 308.00 K THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 48 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 137 DIHEDRAL 137 TORSION ANGLE RESTRAINTS, 198 CH AND 10 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS, AND 200 APPROXIMATE PROTON-PROTON DIPOLAR COUPLINGS. THE EXPERIMENTAL RESTRAINTS ARE THE SAME AS THOSE LISTED IN 1DUF. THE NON-BONDED CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM AND A BASE-BASE POSITIONING DATABASE POTENTIAL OF MEAN FORCE. ALSO INCLUDED IS A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE. IN THIS ENTRY THE SECOND TO LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. MODEL 1 IS CALCULATED WITH NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, DIPOLAR COUPLING RESTRAINTS AND TORSION ANGLE RESTRAINTS. MODEL 2 IS CALCULATED WITH DIPOLAR COUPLING AND TORSION ANGLE RESTRAINTS. NO NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS WERE EMPLOYED. STRUCTURAL STATISTICS: ---------------------------------------------------------- RESTRAINTS MODEL 1 MODEL 2 (# MODEL 1/# MODEL 2) (NOE + DIPOLARS) (DIPOLARS ONLY) ---------------------------------------------------------- RMS DEVIATIONS FROM EXPERIMENTAL RESTRAINTS INTERPROTON DISTANCES (A) 0.065 0.114 (162/0) TORSION ANGLES (DEG) 0 0 (137/137) ALL DIPOLAR COUPLINGS (HZ) 2.8 2.6 (408/408) RMS DEVIATIONS AND DIPOLAR COUPLING R-FACTORS FOR DIFFERENT CLASSES OF DIPOLAR COUPLINGS C-H RIBOSE (HZ/%) (94/94)* 2.27 (11.4%) 2.27 (11.4%) C-H RIBOSE (HZ/%) (64/64)** 5.62 (28.1%) 5.24 (26.2%) C-H BASE (HZ/%) (24/24)* 2.78 (13.9%) 2.81 (14.1%) C-H BASE (HZ/%) (12/12)** 1.89 (9.26%) 2.01 (10.0%) C-H METHYL (HZ/%) (4/4)* 0.98 (4.9%) 0.79 (4.0%) N-H IMINO (HZ/%) (10/10)* 1.56 (15.9%) 1.50 (15.2%) H-H ABSOLUTE VALUE (HZ) (126/126) 1.26 1.25 H-H SIGN KNOWN (HZ) (74/74) 0.93 0.88 RMS DEVIATIONS FROM IDEALIZED COVALENT GEOMETRY BONDS (A) 0.003 0.003 ANGLES (DEG) 0.897 0.925 IMPROPER TORSIONS (DEG) 0.296 0.106 ---------------------------------------------------------- * MEASURED WITH AN ACCURACY OF +/- 2 HZ ** MEASURED WITH AN ACCURACY OF +/- 4 HZ DIPOLAR COUPLING R-FACTOR = RATIO RMS DEVIATION BETWEEN OBSERVED AND CALCULATED VALUES AND EXPECTED RMS DEVIATION IF VECTORS ARE RANDOMLY DISTRIBUTED. THE LATTER IS GIVEN BY {2DA**2[4 + 3H**2]/5}1/2 WHERE DA IS THE MAGNITUDE OF THE AXIAL COMPONENT OF THE ALIGNMENT TENSOR AND H IS THE RHOMBICITY. (ONLY APPLIES TO FIXED LENGTH VECTORS). THE VALUES OF DA(CH), DA(NH) AND H ARE -16 HZ, -7.7 HZ AND 0.26, RESPECTIVELY. SIMULATED ANNEALING IN TORSION ANGLE SPACE USING A SIXTH ORDER PREDICTOR-CORRECTOR METHOD WITH AUTOMATIC TIME STEP SELECTION (C. SCHWIETERS AND G.M. CLORE) 0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0 CLORE, SCHWIETERS AND KUSZEWSKI. ADAPTED FROM XPLOR 3.841 by BRUNGER ET AL. refinement NIH VERSION OF XPLOR (AVAILABLE TO ACADEMIC USERS BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN pub/clore/xplor_nih) structure solution NMRPIPE 1.7 1999.039.11.31 structure solution XwinNMR 2.4 structure solution PIPP/CAPP 4.2.8 600 Bruker DMX 750 Bruker DMX C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A A 5 n 5 DA 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A G 10 n 10 DG 10 A C 11 n 11 DC 11 A G 12 n 12 DG 12 A C 13 n 1 DC 13 B G 14 n 2 DG 14 B C 15 n 3 DC 15 B G 16 n 4 DG 16 B A 17 n 5 DA 17 B A 18 n 6 DA 18 B T 19 n 7 DT 19 B T 20 n 8 DT 20 B C 21 n 9 DC 21 B G 22 n 10 DG 22 B C 23 n 11 DC 23 B G 24 n 12 DG 24 B author_defined_assembly 2 dimeric 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 -3.65 0.60 122.90 119.25 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 -3.66 0.60 122.90 119.24 B B B C6 C5 C7 DT DT DT 20 20 20 N THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE LIQUID CRYSTALLINE PHASE 1 N N 1 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 24 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 24 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 24 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 23 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 23 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 23 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 22 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 21 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 21 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 21 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 20 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 20 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 19 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 19 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 18 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 17 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 16 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 15 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 14 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 14 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 14 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 1 1_555 DNA B-DNA, DIPOLAR COUPLING, NOE, BASE-BASE ORIENTATIONAL POTENTIAL OF MEAN FORCE, DATABASE TORSION ANGLE POTENTIAL OF MEAN FORCE, DNA 1GIP PDB 1 1GIP 1 12 1GIP 1 12 1GIP A 1 1 12 13 24 1GIP 13 24 1GIP B 1 1 12 1 P 1