This structure has broken O3'[i] to P[i+1] linkages **************************************************************************** 3DNA v2.0 [June 8, 2008] (by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com) **************************************************************************** 1. The list of the parameters given below correspond to the 5' to 3' direction of strand I and 3' to 5' direction of strand II. 2. All angular parameters, except for the phase angle of sugar pseudo- rotation, are measured in degrees in the range of [-180, +180], and all displacements are measured in Angstrom units. **************************************************************************** File name: 3exj.pdb Date and time: Thu Apr 5 09:57:21 2018 Number of bases: 23 Number of atoms: 4093 **************************************************************************** HEADER TRANSCRIPTION/DNA 16-OCT-08 3EXJ TITLE CRYSTAL STRUCTURE OF A P53 CORE TETRAMER BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOUSE P53 CORE DOMAIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: P53 CONSENSUS SEQUENCE; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'; COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: P53 CONSENSUS SEQUENCE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, ACETYLATION, ACTIVATOR, ANTI-ONCOGENE, KEYWDS 2 APOPTOSIS, CELL CYCLE, COVALENT PROTEIN-RNA LINKAGE, CYTOPLASM, KEYWDS 3 DISEASE MUTATION, DNA-BINDING, ENDOPLASMIC RETICULUM, METAL-BINDING, KEYWDS 4 METHYLATION, NUCLEUS, PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION KEYWDS 5 REGULATION, UBL CONJUGATION, ZINC, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.A.MALECKA REVDAT 3 25-OCT-17 3EXJ 1 REMARK REVDAT 2 03-FEB-09 3EXJ 1 JRNL REVDAT 1 16-DEC-08 3EXJ 0 JRNL AUTH K.A.MALECKA,W.C.HO,R.MARMORSTEIN JRNL TITL CRYSTAL STRUCTURE OF A P53 CORE TETRAMER BOUND TO DNA. JRNL REF ONCOGENE V. 28 325 2009 JRNL REFN ISSN 0950-9232 JRNL PMID 18978813 JRNL DOI 10.1038/ONC.2008.400 HELIX 1 1 GLN A 101 GLY A 105 5 5 HELIX 2 2 THR A 115 VAL A 119 5 5 HELIX 3 3 CYS A 173 ARG A 178 1 6 HELIX 4 4 CYS A 274 LYS A 288 1 15 HELIX 5 5 GLN B 101 GLY B 105 5 5 HELIX 6 6 THR B 115 VAL B 119 5 5 HELIX 7 7 CYS B 173 ARG B 178 1 6 HELIX 8 8 CYS B 274 ARG B 287 1 14 SHEET 1 A 4 HIS A 107 PHE A 110 0 SHEET 2 A 4 CYS A 138 TRP A 143 -1 O GLN A 141 N GLY A 109 SHEET 3 A 4 THR A 227 TYR A 233 -1 O THR A 227 N LEU A 142 SHEET 4 A 4 ILE A 192 GLU A 195 -1 N GLU A 195 O HIS A 230 SHEET 1 B 7 CYS A 121 SER A 124 0 SHEET 2 B 7 LYS A 129 CYS A 132 -1 O PHE A 131 N THR A 122 SHEET 3 B 7 LEU A 261 VAL A 271 1 O GLU A 268 N LEU A 130 SHEET 4 B 7 ILE A 248 GLU A 255 -1 N LEU A 254 O LEU A 262 SHEET 5 B 7 ARG A 153 TYR A 160 -1 N ARG A 153 O GLU A 255 SHEET 6 B 7 HIS A 211 PRO A 216 -1 O VAL A 215 N VAL A 154 SHEET 7 B 7 GLU A 201 GLU A 204 -1 N LEU A 203 O SER A 212 SHEET 1 C 4 HIS B 107 PHE B 110 0 SHEET 2 C 4 CYS B 138 TRP B 143 -1 O GLN B 141 N GLY B 109 SHEET 3 C 4 THR B 227 TYR B 233 -1 O TYR B 231 N CYS B 138 SHEET 4 C 4 ILE B 192 GLU B 195 -1 N GLU B 195 O HIS B 230 SHEET 1 D 7 CYS B 121 SER B 124 0 SHEET 2 D 7 LYS B 129 CYS B 132 -1 O PHE B 131 N THR B 122 SHEET 3 D 7 LEU B 261 VAL B 271 1 O GLU B 268 N LEU B 130 SHEET 4 D 7 ILE B 248 GLU B 255 -1 N LEU B 254 O LEU B 262 SHEET 5 D 7 ARG B 153 TYR B 160 -1 N MET B 157 O ILE B 251 SHEET 6 D 7 HIS B 211 PRO B 216 -1 O VAL B 215 N VAL B 154 SHEET 7 D 7 GLU B 201 GLU B 204 -1 N LEU B 203 O SER B 212 **************************************************************************** RMSD of the bases Strand I 1 (0.007) ....>C:..13_:[.DG]G- 2 (0.004) ....>C:..14_:[.DA]A- 3 (0.007) ....>C:..15_:[.DG]G- 4 (0.004) ....>C:..16_:[.DC]C- 5 (0.013) ....>C:..17_:[.DA]A- 6 (0.004) ....>C:..18_:[.DT]T- 7 (0.006) ....>C:..19_:[.DG]G- 8 (0.007) ....>C:..20_:[.DC]C- 9 (0.005) ....>C:..21_:[.DT]T- 10 (0.003) ....>C:..22_:[.DC]C- 11 (0.008) ....>C:..23_:[.DA]Ax 12 (0.001) ....>D:...1_:[.DT]T- 13 (0.002) ....>D:...2_:[.DT]T- 14 (0.002) ....>D:...3_:[.DG]G- 15 (0.003) ....>D:...4_:[.DA]A- 16 (0.008) ....>D:...5_:[.DG]G- 17 (0.004) ....>D:...6_:[.DC]C- 18 (0.014) ....>D:...7_:[.DA]A- 19 (0.006) ....>D:...8_:[.DT]T- 20 (0.008) ....>D:...9_:[.DG]G- 21 (0.004) ....>D:..10_:[.DC]C- 22 (0.005) ....>D:..11_:[.DT]T- 23 (0.003) ....>D:..12_:[.DC]C- **************************************************************************** Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step. Values in parentheses measure the overlap of base ring atoms only. Those outside parentheses include exocyclic atoms on the ring. Intra- and inter-strand overlap is designated according to the following diagram: i2 3' /|\ | Strand I | | | | i1 5' step i1-i2 1 G/A 5.00( 2.19) 2 A/G 7.72( 5.46) 3 G/C 4.89( 2.45) 4 C/A 4.87( 1.28) 5 A/T 6.13( 2.38) 6 T/G 0.56( 0.00) 7 G/C 4.79( 2.09) 8 C/T 4.25( 0.00) 9 T/C 4.94( 0.96) 10 C/A 4.40( 0.16) 11 A/T 0.00( 0.00) 12 T/T 3.80( 0.00) 13 T/G 3.33( 0.01) 14 G/A 4.59( 1.50) 15 A/G 7.03( 5.41) 16 G/C 4.84( 2.47) 17 C/A 4.70( 1.33) 18 A/T 6.29( 2.49) 19 T/G 0.22( 0.00) 20 G/C 3.97( 1.63) 21 C/T 4.88( 0.00) 22 T/C 6.55( 1.63) **************************************************************************** Local base step parameters step Shift Slide Rise Tilt Roll Twist 1 G/A -0.04 0.64 2.87 9.79 9.13 33.51 2 A/G 1.20 0.70 3.15 4.36 7.25 33.59 3 G/C 0.95 0.03 3.05 4.81 1.59 39.69 4 C/A 1.82 0.41 3.59 -0.87 4.51 49.51 5 A/T -0.09 -0.29 2.49 19.98 10.09 23.09 6 T/G -0.94 1.04 3.99 -11.76 7.54 31.75 7 G/C 0.25 -0.62 3.72 -5.29 -0.87 40.25 8 C/T -0.70 -0.27 3.48 -0.22 -11.00 32.92 9 T/C 0.84 0.25 2.81 10.90 1.04 39.60 10 C/A 0.08 1.06 2.93 9.99 9.91 28.73 11 A/T -0.29 3.00 0.50 151.72 47.59 -11.82 12 T/T -0.47 -0.82 2.70 12.59 -3.28 31.06 13 T/G 0.07 0.85 3.39 4.30 3.63 31.15 14 G/A -0.18 0.54 3.14 5.18 0.92 39.21 15 A/G 1.14 0.45 3.14 6.45 1.12 36.18 16 G/C 0.68 -0.22 3.15 3.63 1.93 38.18 17 C/A 1.87 0.29 3.72 -4.18 3.57 49.40 18 A/T -0.02 -0.55 2.56 17.62 8.99 27.11 19 T/G -1.06 0.88 3.74 -8.93 3.54 31.63 20 G/C 0.01 -0.49 3.55 -0.83 -2.94 38.50 21 C/T -0.49 0.07 3.45 1.62 -7.15 34.84 22 T/C 0.78 0.62 2.69 14.29 15.35 31.19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.25 0.34 3.08 11.14 5.11 33.15 s.d. 0.82 0.82 0.71 32.43 11.25 11.88 **************************************************************************** Local base helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 G/A -0.14 1.32 2.83 15.11 -16.20 36.01 2 A/G 0.05 -1.34 3.35 12.30 -7.40 34.61 3 G/C -0.13 -0.86 3.14 2.33 -7.05 40.00 4 C/A 0.12 -2.24 3.58 5.37 1.04 49.71 5 A/T -1.87 2.85 1.66 20.14 -39.89 32.05 6 T/G 0.23 -0.79 4.20 13.03 20.31 34.61 7 G/C -0.78 -1.03 3.67 -1.26 7.65 40.59 8 C/T 1.37 1.13 3.40 -18.77 0.38 34.66 9 T/C 0.26 -0.14 2.94 1.50 -15.73 41.02 10 C/A 0.21 1.59 2.99 18.63 -18.77 31.93 11 A/T -1.52 -0.18 -0.57 -26.61 84.83 -159.12 12 T/T -0.98 2.50 2.41 -5.82 -22.33 33.61 13 T/G 0.85 0.70 3.45 6.70 -7.92 31.64 14 G/A 0.70 0.85 3.10 1.37 -7.68 39.55 15 A/G 0.57 -0.94 3.30 1.79 -10.28 36.74 16 G/C -0.57 -0.60 3.18 2.94 -5.53 38.39 17 C/A 0.05 -2.57 3.57 4.26 4.98 49.68 18 A/T -2.09 2.26 1.92 16.66 -32.65 33.45 19 T/G 0.83 0.04 3.95 6.31 15.94 33.02 20 G/C -0.35 -0.13 3.57 -4.45 1.26 38.62 21 C/T 1.20 1.05 3.34 -11.77 -2.66 35.58 22 T/C -0.89 0.51 2.79 25.29 -23.54 37.44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.13 0.18 2.99 3.87 -3.69 28.35 s.d. 0.94 1.45 0.99 12.53 24.49 42.16 **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 0.13(2.31) **************************************************************************** Main chain and chi torsion angles: Note: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) chi for pyrimidines(Y): O4'-C1'-N1-C2 chi for purines(R): O4'-C1'-N9-C4 Strand I base alpha beta gamma delta epsilon zeta chi 1 G --- -113.6 175.3 152.8 -166.3 -122.2 -99.9 2 A 37.4 174.4 -59.9 156.0 162.4 -81.6 -89.0 3 G -62.3 -163.6 43.4 150.3 162.6 -116.8 -81.7 4 C -40.2 174.7 49.9 151.1 172.2 -102.2 -98.6 5 A -57.7 -171.2 51.4 155.0 -157.7 -108.5 -97.0 6 T 6.1 -160.4 -56.7 158.1 -165.4 -149.0 -73.5 7 G -69.2 149.5 66.9 148.9 178.8 -100.3 -115.2 8 C -53.7 -161.7 36.7 148.5 172.1 -114.9 -105.2 9 T -42.1 -175.3 42.9 149.3 177.0 -98.6 -101.4 10 C -50.2 -164.5 30.1 150.3 -176.7 -121.8 -79.2 11 A -50.2 177.1 42.4 157.0 --- --- -74.6 12 T --- --- -62.7 151.9 -159.6 -111.4 -128.9 13 T 35.6 -174.9 -66.8 151.7 -163.8 -68.5 -102.4 14 G -141.8 94.4 154.6 151.6 -171.9 -88.4 -132.9 15 A -78.0 -156.1 43.8 150.3 165.8 -97.1 -87.4 16 G -49.9 -172.3 44.5 150.6 169.5 -121.9 -84.6 17 C -40.2 173.9 46.5 150.7 175.2 -106.4 -99.1 18 A -57.0 -179.4 53.8 154.4 -155.3 -119.5 -104.2 19 T 18.8 -176.2 -59.2 158.9 -163.7 -157.2 -76.9 20 G -60.0 146.2 59.9 149.3 -179.5 -105.0 -115.0 21 C -54.1 -163.2 37.7 150.0 170.4 -118.5 -99.6 22 T -45.2 -176.1 48.7 151.7 -168.4 -121.8 -98.1 23 C 43.4 151.6 -54.5 158.6 --- --- -65.5 **************************************************************************** Sugar conformational parameters: Note: v0: C4'-O4'-C1'-C2' v1: O4'-C1'-C2'-C3' v2: C1'-C2'-C3'-C4' v3: C2'-C3'-C4'-O4' v4: C3'-C4'-O4'-C1' tm: amplitude of pseudorotation of the sugar ring P: phase angle of pseudorotation of the sugar ring Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 G -6.5 26.0 -34.4 31.4 -15.8 34.8 187.9 C3'-exo 2 A -1.3 21.6 -32.3 32.0 -19.4 33.6 196.0 C3'-exo 3 G -12.8 31.5 -37.1 30.7 -11.3 37.1 178.8 C2'-endo 4 C -14.8 32.7 -37.2 29.8 -9.5 37.3 175.9 C2'-endo 5 A -13.0 31.5 -37.0 30.7 -11.2 37.1 178.7 C2'-endo 6 T -8.3 27.8 -35.5 31.6 -14.7 35.7 185.3 C3'-exo 7 G -14.4 31.9 -36.6 29.1 -9.3 36.7 175.9 C2'-endo 8 C -10.4 29.1 -35.8 30.5 -12.8 35.8 182.0 C3'-exo 9 T -12.5 30.6 -36.3 29.9 -11.1 36.3 178.9 C2'-endo 10 C -12.7 30.8 -36.3 29.8 -10.8 36.3 178.5 C2'-endo 11 A -14.1 32.4 -37.4 30.3 -10.3 37.4 177.1 C2'-endo 12 T -8.9 27.5 -34.6 30.1 -13.5 34.7 183.9 C3'-exo 13 T -5.8 24.7 -33.1 30.3 -15.5 33.4 188.5 C3'-exo 14 G -7.3 26.3 -34.2 30.6 -14.8 34.4 186.4 C3'-exo 15 A -9.6 28.1 -35.0 30.1 -13.0 35.0 182.9 C3'-exo 16 G -14.1 32.4 -37.3 30.3 -10.3 37.3 177.0 C2'-endo 17 C -16.0 33.7 -37.5 29.5 -8.6 37.7 174.3 C2'-endo 18 A -14.9 33.0 -37.4 30.0 -9.6 37.5 175.9 C2'-endo 19 T -8.8 28.3 -35.7 31.6 -14.4 35.8 184.6 C3'-exo 20 G -14.3 32.0 -36.8 29.4 -9.6 36.9 176.4 C2'-endo 21 C -11.4 30.0 -36.1 30.4 -12.0 36.2 180.5 C3'-exo 22 T -12.3 30.5 -36.3 30.1 -11.4 36.3 179.3 C2'-endo 23 C -7.6 26.8 -34.6 31.0 -14.8 34.8 186.1 C3'-exo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I step P--P C1'--C1' 1 G/A 7.2 5.3 2 A/G 6.9 4.5 3 G/C 6.8 4.7 4 C/A 6.9 4.9 5 A/T 6.7 5.4 6 T/G 6.6 5.1 7 G/C 7.2 5.2 8 C/T 6.6 5.1 9 T/C 6.7 5.0 10 C/A 6.4 5.1 11 A/T --- 12.4 12 T/T --- 5.4 13 T/G 6.6 4.9 14 G/A 7.3 5.4 15 A/G 6.5 4.6 16 G/C 6.8 4.9 17 C/A 6.9 4.8 18 A/T 6.8 5.4 19 T/G 6.6 5.0 20 G/C 7.2 5.3 21 C/T 6.6 5.2 22 T/C 6.7 5.2 **************************************************************************** Helix radius (radial displacement of P, O4', and C1' atoms in local helix frame of each dimer) step P O4' C1' 1 G/A 10.9 7.7 7.1 2 A/G 8.1 5.2 4.7 3 G/C 8.3 5.7 5.2 4 C/A 6.9 4.5 3.9 5 A/T 12.9 9.6 9.2 6 T/G 7.9 5.6 4.7 7 G/C 8.6 6.1 5.5 8 C/T 9.6 6.4 6.3 9 T/C 9.1 5.9 5.7 10 C/A 10.6 7.7 7.2 11 A/T ---- 7.2 6.3 12 T/T 12.2 8.8 8.4 13 T/G 10.0 7.1 6.3 14 G/A 9.7 7.1 6.5 15 A/G 8.3 5.1 4.8 16 G/C 8.8 6.2 5.7 17 C/A 6.6 4.3 3.7 18 A/T 12.5 9.2 8.8 19 T/G 8.8 6.2 5.5 20 G/C 9.2 6.5 6.0 21 C/T 9.6 6.6 6.4 22 T/C 10.3 7.2 6.7 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) step Px Py Pz Hx Hy Hz 1 G/A -1.45 32.45 3.50 -0.40 -0.00 0.92 2 A/G -1.60 34.78 6.83 -0.53 0.05 0.85 3 G/C -3.29 34.19 9.79 -0.54 -0.12 0.83 4 C/A -6.15 34.64 11.86 -0.65 -0.17 0.74 5 A/T -3.76 36.41 16.78 -0.70 0.53 0.48 6 T/G -7.78 33.04 18.45 -0.36 -0.33 0.87 7 G/C -10.28 32.71 21.77 -0.42 -0.00 0.91 8 C/T -10.01 35.45 25.50 -0.52 0.29 0.80 9 T/C -12.03 34.09 28.47 -0.54 -0.16 0.82 10 C/A -14.89 33.74 30.60 -0.29 -0.27 0.92 11 A/T -14.87 33.16 33.60 -0.46 0.83 -0.31 12 T/T -12.86 34.06 35.43 0.67 -0.26 -0.69 13 T/G -12.80 34.61 31.28 0.46 -0.10 -0.88 14 G/A -11.13 34.07 28.60 0.53 -0.12 -0.84 15 A/G -10.41 34.96 25.09 0.50 -0.14 -0.86 16 G/C -9.66 34.16 21.83 0.57 -0.12 -0.81 17 C/A -6.15 34.84 20.16 0.69 -0.20 -0.70 18 A/T -8.19 36.45 15.27 0.72 0.45 -0.53 19 T/G -5.53 33.08 12.94 0.39 -0.22 -0.89 20 G/C -2.90 33.30 9.99 0.49 0.08 -0.87 21 C/T -2.51 35.01 6.46 0.54 0.20 -0.82 22 T/C 0.24 32.99 4.45 0.40 -0.51 -0.76