0.015011 0.008667 0.000000 0.000000 0.017334 0.000000 0.000000 0.000000 0.021517 0.000000 0.000000 0.000000 Nedyalkova, L. Tong, Y. Tempel, W. Zhong, N. Guan, X. Landry, R. Arrowsmith, C.H. Edwards, A.M. Bountra, C. Weigelt, J. Bochkarev, A. Park, H. Structural Genomics Consortium (SGC) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.000 90.000 120.000 66.616 66.616 46.475 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking UNKNOWN ATOM OR ION non-polymer C5 H11 N O2 117.146 y VALINE L-peptide linking TO BE PUBLISHED 0353 Crystal structure of the PDZ domain of MPP7 100 1 100 1 CCD 2010-06-17 ADSC QUANTUM 315 IMAGE PLATE 2010-06-13 RIGAKU RAXIS SINGLE WAVELENGTH M x-ray 1 SINGLE WAVELENGTH M x-ray 1 0.97904 1.0 1.5418 1.0 19-ID APS 0.97904 SYNCHROTRON APS BEAMLINE 19-ID 1.5418 ROTATING ANODE RIGAKU FR-E DW 10102.445 MAGUK p55 subfamily member 7 PDZ Domain (UNP residues 135-225) 1 man polymer UNKNOWN ATOM OR ION 13 syn non-polymer 18.015 water 69 nat water no yes GSDSVKIIRLVKNREPLGATIKKDEQTGAIIVARI(MSE)RGGAADRSGLIHVGDELREVNGIPVEDKRPEEIIQILAQS QGAITFKIIPGSKEETP GSDSVKIIRLVKNREPLGATIKKDEQTGAIIVARIMRGGAADRSGLIHVGDELREVNGIPVEDKRPEEIIQILAQSQGAI TFKIIPGSKEETP A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample MPP7 9606 Homo sapiens 511693 Escherichia coli BL21-V2R-pRARE2 pET28a-LIC 1 2.95 58.26 VAPOR DIFFUSION, SITTING DROP 7.5 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K 291 Structural Genomics Consortium SGC software repository Initial release Version format compliance Refinement description 1 0 2010-08-04 1 1 2011-07-13 1 2 2017-11-08 Y RCSB Y RCSB 2010-07-26 REL REL UNX UNKNOWN ATOM OR ION HOH water UNX 1 2 UNX UNX 1 A UNX 2 2 UNX UNX 2 A UNX 3 2 UNX UNX 3 A UNX 4 2 UNX UNX 4 A UNX 5 2 UNX UNX 5 A UNX 6 2 UNX UNX 6 A UNX 7 2 UNX UNX 7 A UNX 8 2 UNX UNX 8 A UNX 9 2 UNX UNX 9 A UNX 10 2 UNX UNX 10 A UNX 11 2 UNX UNX 11 A UNX 12 2 UNX UNX 12 A UNX 13 2 UNX UNX 13 A HOH 14 3 HOH HOH 14 A HOH 15 3 HOH HOH 15 A HOH 16 3 HOH HOH 16 A HOH 17 3 HOH HOH 17 A HOH 18 3 HOH HOH 18 A HOH 19 3 HOH HOH 19 A HOH 20 3 HOH HOH 20 A HOH 21 3 HOH HOH 21 A HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 24 3 HOH HOH 24 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 32 3 HOH HOH 32 A HOH 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 35 3 HOH HOH 35 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 39 3 HOH HOH 39 A HOH 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 43 3 HOH HOH 43 A HOH 44 3 HOH HOH 44 A HOH 45 3 HOH HOH 45 A HOH 46 3 HOH HOH 46 A HOH 47 3 HOH HOH 47 A HOH 48 3 HOH HOH 48 A HOH 49 3 HOH HOH 49 A HOH 50 3 HOH HOH 50 A HOH 51 3 HOH HOH 51 A HOH 52 3 HOH HOH 52 A HOH 53 3 HOH HOH 53 A HOH 54 3 HOH HOH 54 A HOH 55 3 HOH HOH 55 A HOH 56 3 HOH HOH 56 A HOH 57 3 HOH HOH 57 A HOH 58 3 HOH HOH 58 A HOH 59 3 HOH HOH 59 A HOH 60 3 HOH HOH 60 A HOH 61 3 HOH HOH 61 A HOH 62 3 HOH HOH 62 A HOH 63 3 HOH HOH 63 A HOH 64 3 HOH HOH 64 A HOH 65 3 HOH HOH 65 A HOH 66 3 HOH HOH 66 A HOH 67 3 HOH HOH 67 A HOH 68 3 HOH HOH 68 A HOH 69 3 HOH HOH 69 A HOH 1 3 HOH HOH 226 A HOH 2 3 HOH HOH 227 A HOH 3 3 HOH HOH 228 A HOH 4 3 HOH HOH 229 A HOH 5 3 HOH HOH 230 A HOH 6 3 HOH HOH 231 A HOH 7 3 HOH HOH 232 A HOH 8 3 HOH HOH 233 A HOH 9 3 HOH HOH 234 A HOH 10 3 HOH HOH 235 A HOH 11 3 HOH HOH 236 A HOH 12 3 HOH HOH 237 A HOH 13 3 HOH HOH 238 A n 1 133 A n 2 134 A n 3 135 A SER 136 n 4 SER 136 A VAL 137 n 5 VAL 137 A LYS 138 n 6 LYS 138 A ILE 139 n 7 ILE 139 A ILE 140 n 8 ILE 140 A ARG 141 n 9 ARG 141 A LEU 142 n 10 LEU 142 A VAL 143 n 11 VAL 143 A LYS 144 n 12 LYS 144 A ASN 145 n 13 ASN 145 A ARG 146 n 14 ARG 146 A GLU 147 n 15 GLU 147 A PRO 148 n 16 PRO 148 A LEU 149 n 17 LEU 149 A GLY 150 n 18 GLY 150 A ALA 151 n 19 ALA 151 A THR 152 n 20 THR 152 A ILE 153 n 21 ILE 153 A LYS 154 n 22 LYS 154 A LYS 155 n 23 LYS 155 A ASP 156 n 24 ASP 156 A GLU 157 n 25 GLU 157 A GLN 158 n 26 GLN 158 A THR 159 n 27 THR 159 A GLY 160 n 28 GLY 160 A ALA 161 n 29 ALA 161 A ILE 162 n 30 ILE 162 A ILE 163 n 31 ILE 163 A VAL 164 n 32 VAL 164 A ALA 165 n 33 ALA 165 A ARG 166 n 34 ARG 166 A ILE 167 n 35 ILE 167 A MSE 168 n 36 MSE 168 A ARG 169 n 37 ARG 169 A GLY 170 n 38 GLY 170 A GLY 171 n 39 GLY 171 A ALA 172 n 40 ALA 172 A ALA 173 n 41 ALA 173 A ASP 174 n 42 ASP 174 A ARG 175 n 43 ARG 175 A SER 176 n 44 SER 176 A GLY 177 n 45 GLY 177 A LEU 178 n 46 LEU 178 A ILE 179 n 47 ILE 179 A HIS 180 n 48 HIS 180 A VAL 181 n 49 VAL 181 A GLY 182 n 50 GLY 182 A ASP 183 n 51 ASP 183 A GLU 184 n 52 GLU 184 A LEU 185 n 53 LEU 185 A ARG 186 n 54 ARG 186 A GLU 187 n 55 GLU 187 A VAL 188 n 56 VAL 188 A ASN 189 n 57 ASN 189 A GLY 190 n 58 GLY 190 A ILE 191 n 59 ILE 191 A PRO 192 n 60 PRO 192 A VAL 193 n 61 VAL 193 A GLU 194 n 62 GLU 194 A ASP 195 n 63 ASP 195 A LYS 196 n 64 LYS 196 A ARG 197 n 65 ARG 197 A PRO 198 n 66 PRO 198 A GLU 199 n 67 GLU 199 A GLU 200 n 68 GLU 200 A ILE 201 n 69 ILE 201 A ILE 202 n 70 ILE 202 A GLN 203 n 71 GLN 203 A ILE 204 n 72 ILE 204 A LEU 205 n 73 LEU 205 A ALA 206 n 74 ALA 206 A GLN 207 n 75 GLN 207 A SER 208 n 76 SER 208 A GLN 209 n 77 GLN 209 A GLY 210 n 78 GLY 210 A ALA 211 n 79 ALA 211 A ILE 212 n 80 ILE 212 A THR 213 n 81 THR 213 A PHE 214 n 82 PHE 214 A LYS 215 n 83 LYS 215 A ILE 216 n 84 ILE 216 A ILE 217 n 85 ILE 217 A PRO 218 n 86 PRO 218 A GLY 219 n 87 GLY 219 A n 88 220 A n 89 221 A n 90 222 A n 91 223 A n 92 224 A n 93 225 A software_defined_assembly PISA 3 trimeric 4210 -16 11230 A MSE 168 SELENOMETHIONINE A MSE 36 MET 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 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_665 -y+1,x-y+1,z crystal symmetry operation 33.3080000000 57.6911482985 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_565 -x+y,-x+1,z crystal symmetry operation -33.3080000000 57.6911482985 0.0000000000 A N LEU 142 A N LEU 10 A O ILE 212 A O ILE 80 A O LYS 215 A O LYS 83 A N ARG 186 A N ARG 54 A O LEU 185 A O LEU 53 A N ILE 162 A N ILE 30 A O ALA 165 A O ALA 33 A N THR 152 A N THR 20 A N LEU 142 A N LEU 10 A O ILE 212 A O ILE 80 A O LYS 215 A O LYS 83 A N ARG 186 A N ARG 54 A N VAL 188 A N VAL 56 A O ILE 191 A O ILE 59 1 A HOH 33 O HOH 1 A HOH 49 O HOH 1 A CE LYS 138 A CE LYS 6 1 Y 1 A NZ LYS 138 A NZ LYS 6 1 Y 1 A NE ARG 146 A NE ARG 14 1 Y 1 A CZ ARG 146 A CZ ARG 14 1 Y 1 A NH1 ARG 146 A NH1 ARG 14 1 Y 1 A NH2 ARG 146 A NH2 ARG 14 1 Y 1 A NZ LYS 154 A NZ LYS 22 1 Y 1 A CD GLU 157 A CD GLU 25 1 Y 1 A OE1 GLU 157 A OE1 GLU 25 1 Y 1 A OE2 GLU 157 A OE2 GLU 25 1 Y 1 A CG ARG 169 A CG ARG 37 1 Y 1 A CD ARG 169 A CD ARG 37 1 Y 1 A NE ARG 169 A NE ARG 37 1 Y 1 A CZ ARG 169 A CZ ARG 37 1 Y 1 A NH1 ARG 169 A NH1 ARG 37 1 Y 1 A NH2 ARG 169 A NH2 ARG 37 1 Y 1 A NE ARG 197 A NE ARG 65 1 Y 1 A CZ ARG 197 A CZ ARG 65 1 Y 1 A NH1 ARG 197 A NH1 ARG 65 1 Y 1 A NH2 ARG 197 A NH2 ARG 65 1 Y 1 A CE LYS 215 A CE LYS 83 1 Y 1 A NZ LYS 215 A NZ LYS 83 1 Y 1 A GLY 133 A GLY 1 1 Y 1 A SER 134 A SER 2 1 Y 1 A ASP 135 A ASP 3 1 Y 1 A SER 220 A SER 88 1 Y 1 A LYS 221 A LYS 89 1 Y 1 A GLU 222 A GLU 90 1 Y 1 A GLU 223 A GLU 91 1 Y 1 A THR 224 A THR 92 1 Y 1 A PRO 225 A PRO 93 1 Y 1 A A VAL GLU 193 194 -149.07 44.670 12.9910 9.100 0.5840 0.2920 0.0000 0.5840 0.0000 -0.8760 0.9590 0.9580 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY . The structure was originally solved using data measured with the same crystal on a copper rotating anode. The model was refined against higher resolution synchrotron data. Scaled synchrotron intensities have been deposited along with the structure factors. 0.1908 0.1839 0.1840 1.3000 33.3080 1449 28929 5.0090 99.8070 0.1950 0.1920 1.000 0.010 1.1950 0.0240 RANDOM 2 THROUGHOUT 0.000 SAD 0.046 0.0420 0.8000 0.8000 1.4000 MAXIMUM LIKELIHOOD MASK BULK SOLVENT 1.3000 33.3080 69 699 13 0 617 0.018 0.022 700 0.002 0.020 493 1.679 1.987 963 0.921 3.000 1231 6.733 5.000 105 36.165 25.000 26 10.900 15.000 140 6.682 15.000 5 0.110 0.200 119 0.008 0.021 792 0.001 0.020 121 1.902 1.500 453 0.565 1.500 185 2.973 2.000 749 3.989 3.000 247 6.028 4.500 203 1.413 3.000 1193 0.238 0.217 1.334 114 2020 2137 20 99.860 0.221 0.196 1.370 103 1972 2075 20 100.000 0.164 0.169 1.410 131 1877 2012 20 99.801 0.210 0.166 1.453 96 1866 1964 20 99.898 0.165 0.145 1.501 113 1785 1900 20 99.895 0.185 0.152 1.553 84 1745 1832 20 99.836 0.207 0.155 1.612 84 1689 1774 20 99.944 0.151 0.153 1.677 76 1647 1725 20 99.884 0.188 0.158 1.752 75 1565 1641 20 99.939 0.168 0.159 1.837 73 1496 1571 20 99.873 0.206 0.157 1.936 74 1421 1497 20 99.866 0.187 0.155 2.053 60 1337 1399 20 99.857 0.156 0.155 2.194 84 1257 1342 20 99.925 0.122 0.150 2.369 47 1199 1246 20 100.000 0.203 0.187 2.594 55 1093 1151 20 99.739 0.187 0.200 2.898 37 1007 1045 20 99.904 0.192 0.215 3.342 53 856 909 20 100.000 0.199 0.195 4.083 34 752 786 20 100.000 0.206 0.196 5.731 35 581 619 20 99.515 0.310 0.324 33.308 21 315 360 20 93.333 1.300 40.000 3O46 28982 0.041 1.566 2,1 14.600 5.600 99.800 0.751 1.300 1.320 2847 1.660 5.500 100.000 0.663 1.320 1.350 2815 1.599 5.500 99.800 0.522 1.350 1.370 2882 1.610 5.500 99.900 0.421 1.370 1.400 2844 1.514 5.500 100.000 0.369 1.400 1.430 2821 1.491 5.500 99.900 0.320 1.430 1.460 2850 1.453 5.600 99.900 0.231 1.460 1.500 2899 1.410 5.600 99.900 0.189 1.500 1.540 2812 1.430 5.600 100.000 0.159 1.540 1.590 2852 1.419 5.600 100.000 0.128 1.590 1.640 2801 1.389 5.600 100.000 0.101 1.640 1.700 2904 1.441 5.600 100.000 0.084 1.700 1.760 2837 1.409 5.600 100.000 0.068 1.760 1.840 2877 1.459 5.700 100.000 0.054 1.840 1.940 2835 1.587 5.700 100.000 0.053 1.940 2.060 2809 2.031 5.700 100.000 0.049 2.060 2.220 2885 2.329 5.600 100.000 0.040 2.220 2.450 2849 1.918 5.600 100.000 0.030 2.450 2.800 2865 1.429 5.500 100.000 0.027 2.800 3.530 2837 1.419 5.800 100.000 0.025 3.530 40.000 2800 1.308 5.500 97.700 data reduction Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ DENZO package data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK package phasing George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.5.0109 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 phasing SHELXDE N MAGUK p55 subfamily member 7 Crystal structure of the PDZ domain of MPP7 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N A GLY 171 A GLY 39 HELX_P A GLY 177 A GLY 45 1 1 7 A ARG 197 A ARG 65 HELX_P A SER 208 A SER 76 1 2 12 covale 1.315 A ILE 167 A C ILE 35 1_555 A MSE 168 A N MSE 36 1_555 covale 1.342 A MSE 168 A C MSE 36 1_555 A ARG 169 A N ARG 37 1_555 PROTEIN BINDING pdz domain, structural genomics consortium, SGC, PROTEIN BINDING MPP7_HUMAN UNP 1 135 Q5T2T1 DSVKIIRLVKNREPLGATIKKDEQTGAIIVARIMRGGAADRSGLIHVGDELREVNGIPVEDKRPEEIIQILAQSQGAITF KIIPGSKEETP 135 225 3O46 135 225 Q5T2T1 A 1 3 93 1 EXPRESSION TAG GLY 133 3O46 A Q5T2T1 UNP 1 1 EXPRESSION TAG SER 134 3O46 A Q5T2T1 UNP 2 5 4 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A LYS 138 A LYS 6 A LYS 144 A LYS 12 A GLY 210 A GLY 78 A ILE 217 A ILE 85 A GLU 184 A GLU 52 A VAL 188 A VAL 56 A ILE 162 A ILE 30 A ILE 167 A ILE 35 A ALA 151 A ALA 19 A LYS 155 A LYS 23 A LYS 138 A LYS 6 A LYS 144 A LYS 12 A GLY 210 A GLY 78 A ILE 217 A ILE 85 A GLU 184 A GLU 52 A VAL 188 A VAL 56 A ILE 191 A ILE 59 A PRO 192 A PRO 60 173 P 63