0.013757 0.007943 0.000000 0.000000 0.015885 0.000000 0.000000 0.000000 0.018832 0.000000 0.000000 0.000000 Chattopadhyay, K. Ramagopal, U.A. Nathenson, S.G. Almo, S.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.000 90.000 120.000 72.691 72.691 53.101 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 C3 H7 N O2 S 121.158 y CYSTEINE 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 S 149.211 y METHIONINE 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 C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 104 19452 19457 10.1073/pnas.0709264104 18040044 Assembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function. 2007 100 1 1 CCD 2006-04-08 ADSC QUANTUM 4 CCD 2006-04-16 ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 SINGLE WAVELENGTH M x-ray 1 0.9795 1.0 1.009 1.0 6.10 180253 0.120 1.05 2.500 50.000 10652 100.00 16.90 X4A NSLS 0.9795 SYNCHROTRON NSLS BEAMLINE X4A X29A NSLS 1.009 SYNCHROTRON NSLS BEAMLINE X29A 14687.742 Tumor necrosis factor ligand superfamily member 18 Extracellular, TNF homology domain 1 man polymer 18.015 water 42 nat water Glucocorticoid-induced TNF-related ligand, hGITRL, Activation-inducible TNF-related ligand, AITRL no no GSHMETAKEPCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTL TNKSKIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLANPQFIS GSHMETAKEPCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTL TNKSKIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLANPQFIS 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 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 Homo Escherichia sample TNFSF18, AITRL, GITRL, TL6 9606 Homo sapiens 562 Escherichia coli Rosetta (DE3) pLysS plasmid pET-14b 1 2.76 55.37 VAPOR DIFFUSION, SITTING DROP 4.5 25% PEG 3350, 0.1 M Sodium Acetate pH 4.5, Vapor diffusion, Sitting drop, temperature 298K 298 software repository Initial release Version format compliance Refinement description 1 0 2007-11-13 1 1 2011-07-13 1 2 2017-10-18 RCSB Y RCSB 2007-05-24 REL REL 0.080 2.092 99.80 16.60 0.094 1.970 99.90 16.50 0.107 1.850 100.00 16.90 0.119 1.380 100.00 17.10 0.169 0.888 100.00 17.00 0.237 0.645 100.00 17.10 0.343 0.515 100.00 17.20 0.519 0.436 100.00 17.10 0.679 0.411 100.00 17.00 0.373 100.00 16.70 HOH water HOH 1 2 HOH HOH 178 A HOH 2 2 HOH HOH 179 A HOH 3 2 HOH HOH 180 A HOH 4 2 HOH HOH 181 A HOH 5 2 HOH HOH 182 A HOH 6 2 HOH HOH 183 A HOH 7 2 HOH HOH 184 A HOH 8 2 HOH HOH 185 A HOH 10 2 HOH HOH 186 A HOH 11 2 HOH HOH 187 A HOH 12 2 HOH HOH 188 A HOH 13 2 HOH HOH 189 A HOH 15 2 HOH HOH 190 A HOH 16 2 HOH HOH 191 A HOH 17 2 HOH HOH 192 A HOH 18 2 HOH HOH 193 A HOH 19 2 HOH HOH 194 A HOH 20 2 HOH HOH 195 A HOH 21 2 HOH HOH 196 A HOH 22 2 HOH HOH 197 A HOH 23 2 HOH HOH 198 A HOH 24 2 HOH HOH 199 A HOH 25 2 HOH HOH 200 A HOH 26 2 HOH HOH 201 A HOH 27 2 HOH HOH 202 A HOH 28 2 HOH HOH 203 A HOH 30 2 HOH HOH 204 A HOH 31 2 HOH HOH 205 A HOH 32 2 HOH HOH 206 A HOH 37 2 HOH HOH 207 A HOH 40 2 HOH HOH 208 A HOH 50 2 HOH HOH 209 A HOH 52 2 HOH HOH 210 A HOH 54 2 HOH HOH 211 A HOH 56 2 HOH HOH 212 A HOH 57 2 HOH HOH 213 A HOH 58 2 HOH HOH 214 A HOH 62 2 HOH HOH 215 A HOH 66 2 HOH HOH 216 A HOH 71 2 HOH HOH 217 A HOH 74 2 HOH HOH 218 A HOH 79 2 HOH HOH 219 A n 1 48 A n 2 49 A n 3 50 A n 4 51 A n 5 52 A n 6 53 A n 7 54 A n 8 55 A n 9 56 A PRO 57 n 10 PRO 57 A CYS 58 n 11 CYS 58 A MET 59 n 12 MET 59 A ALA 60 n 13 ALA 60 A LYS 61 n 14 LYS 61 A PHE 62 n 15 PHE 62 A GLY 63 n 16 GLY 63 A PRO 64 n 17 PRO 64 A LEU 65 n 18 LEU 65 A PRO 66 n 19 PRO 66 A SER 67 n 20 SER 67 A LYS 68 n 21 LYS 68 A TRP 69 n 22 TRP 69 A GLN 70 n 23 GLN 70 A MET 71 n 24 MET 71 A ALA 72 n 25 ALA 72 A SER 73 n 26 SER 73 A SER 74 n 27 SER 74 A GLU 75 n 28 GLU 75 A PRO 76 n 29 PRO 76 A PRO 77 n 30 PRO 77 A CYS 78 n 31 CYS 78 A VAL 79 n 32 VAL 79 A ASN 80 n 33 ASN 80 A LYS 81 n 34 LYS 81 A VAL 82 n 35 VAL 82 A SER 83 n 36 SER 83 A ASP 84 n 37 ASP 84 A TRP 85 n 38 TRP 85 A LYS 86 n 39 LYS 86 A LEU 87 n 40 LEU 87 A GLU 88 n 41 GLU 88 A ILE 89 n 42 ILE 89 A LEU 90 n 43 LEU 90 A GLN 91 n 44 GLN 91 A ASN 92 n 45 ASN 92 A GLY 93 n 46 GLY 93 A LEU 94 n 47 LEU 94 A TYR 95 n 48 TYR 95 A LEU 96 n 49 LEU 96 A ILE 97 n 50 ILE 97 A TYR 98 n 51 TYR 98 A GLY 99 n 52 GLY 99 A GLN 100 n 53 GLN 100 A VAL 101 n 54 VAL 101 A ALA 102 n 55 ALA 102 A PRO 103 n 56 PRO 103 A ASN 104 n 57 ASN 104 A ALA 105 n 58 ALA 105 A ASN 106 n 59 ASN 106 A TYR 107 n 60 TYR 107 A ASN 108 n 61 ASN 108 A ASP 109 n 62 ASP 109 A VAL 110 n 63 VAL 110 A ALA 111 n 64 ALA 111 A PRO 112 n 65 PRO 112 A PHE 113 n 66 PHE 113 A GLU 114 n 67 GLU 114 A VAL 115 n 68 VAL 115 A ARG 116 n 69 ARG 116 A LEU 117 n 70 LEU 117 A TYR 118 n 71 TYR 118 A LYS 119 n 72 LYS 119 A ASN 120 n 73 ASN 120 A LYS 121 n 74 LYS 121 A ASP 122 n 75 ASP 122 A MET 123 n 76 MET 123 A ILE 124 n 77 ILE 124 A GLN 125 n 78 GLN 125 A THR 126 n 79 THR 126 A LEU 127 n 80 LEU 127 A THR 128 n 81 THR 128 A ASN 129 n 82 ASN 129 A LYS 130 n 83 LYS 130 A SER 131 n 84 SER 131 A LYS 132 n 85 LYS 132 A ILE 133 n 86 ILE 133 A GLN 134 n 87 GLN 134 A ASN 135 n 88 ASN 135 A VAL 136 n 89 VAL 136 A GLY 137 n 90 GLY 137 A GLY 138 n 91 GLY 138 A THR 139 n 92 THR 139 A TYR 140 n 93 TYR 140 A GLU 141 n 94 GLU 141 A LEU 142 n 95 LEU 142 A HIS 143 n 96 HIS 143 A VAL 144 n 97 VAL 144 A GLY 145 n 98 GLY 145 A ASP 146 n 99 ASP 146 A THR 147 n 100 THR 147 A ILE 148 n 101 ILE 148 A ASP 149 n 102 ASP 149 A LEU 150 n 103 LEU 150 A ILE 151 n 104 ILE 151 A PHE 152 n 105 PHE 152 A ASN 153 n 106 ASN 153 A SER 154 n 107 SER 154 A GLU 155 n 108 GLU 155 A HIS 156 n 109 HIS 156 A GLN 157 n 110 GLN 157 A VAL 158 n 111 VAL 158 A LEU 159 n 112 LEU 159 A LYS 160 n 113 LYS 160 A ASN 161 n 114 ASN 161 A ASN 162 n 115 ASN 162 A THR 163 n 116 THR 163 A TYR 164 n 117 TYR 164 A TRP 165 n 118 TRP 165 A GLY 166 n 119 GLY 166 A ILE 167 n 120 ILE 167 A ILE 168 n 121 ILE 168 A LEU 169 n 122 LEU 169 A LEU 170 n 123 LEU 170 A ALA 171 n 124 ALA 171 A ASN 172 n 125 ASN 172 A n 126 173 A n 127 174 A n 128 175 A n 129 176 A n 130 177 A author_defined_assembly 3 trimeric 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_655 -y+1,x-y,z crystal symmetry operation 72.6910000000 0.0000000000 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_665 -x+y+1,-x+1,z crystal symmetry operation 36.3455000000 62.9522526265 0.0000000000 A O GLN 70 A O GLN 23 A N LYS 61 A N LYS 14 A N PHE 62 A N PHE 15 A O TRP 165 A O TRP 118 A O LEU 170 A O LEU 123 A N LEU 94 A N LEU 47 A N VAL 101 A N VAL 54 A O GLN 134 A O GLN 87 A O GLN 70 A O GLN 23 A N LYS 61 A N LYS 14 A N PHE 62 A N PHE 15 A O TRP 165 A O TRP 118 A O LEU 170 A O LEU 123 A N LEU 94 A N LEU 47 A N ILE 97 A N ILE 50 A O GLY 138 A O GLY 91 A N SER 83 A N SER 36 A O LYS 86 A O LYS 39 A N LEU 87 A N LEU 40 A O ILE 148 A O ILE 101 A O ASP 149 A O ASP 102 A N TYR 118 A N TYR 71 A N LEU 117 A N LEU 70 A O ILE 124 A O ILE 77 1 A GLY 48 A GLY 1 1 Y 1 A SER 49 A SER 2 1 Y 1 A HIS 50 A HIS 3 1 Y 1 A MET 51 A MET 4 1 Y 1 A GLU 52 A GLU 5 1 Y 1 A THR 53 A THR 6 1 Y 1 A ALA 54 A ALA 7 1 Y 1 A LYS 55 A LYS 8 1 Y 1 A GLU 56 A GLU 9 1 Y 1 A PRO 173 A PRO 126 1 Y 1 A GLN 174 A GLN 127 1 Y 1 A PHE 175 A PHE 128 1 Y 1 A ILE 176 A ILE 129 1 Y 1 A SER 177 A SER 130 1 Y 1 A LYS 68 -105.78 -125.69 1 A ASN 106 -89.95 35.61 1 A ASN 120 57.48 -123.92 1 A ASN 162 -140.60 25.00 44.570 0.640 0.320 0.000 0.640 0.000 -0.960 0.949 0.920 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.257 0.215 0.217 0.217 2.300 21.7 331 7117 7117 4.700 99.410 6.671 0.164 RANDOM 1 THROUGHOUT 0.00 0 SAD 0.299 0.230 0.800 0.800 1.400 MAXIMUM LIKELIHOOD MASK 2.300 21.7 42 989 0 0 947 0.012 0.022 974 1.431 1.950 1331 7.327 5.000 121 37.981 26.522 46 17.099 15.000 167 18.478 15.000 1 0.087 0.200 145 0.005 0.020 748 0.200 0.200 402 0.311 0.200 643 0.134 0.200 51 0.249 0.200 29 0.173 0.200 6 0.899 1.500 615 1.539 2.000 968 1.635 3.000 424 2.444 4.500 362 0.407 0.320 2.363 17 465 482 20 93.050 2.300 21.7 2Q1M 7131 7131 0 0 0.071 1.296 1,2 10.500 10.800 99.900 2.30 2.38 693 1.029 10.80 100.00 data reduction Zbyszek Otwinowski zbyszek@mix.swmed.edu http://www.lnls.br/infra/linhasluz/denzo-hkl.htm DENZO package data scaling Zbyszek Otwinowski zbyszek@mix.swmed.edu http://www.lnls.br/infra/linhasluz/denzo-hkl.htm SCALEPACK package refinement Murshudov, G.N. ccp4@dl.ac.uk Fortran_77 http://www.ccp4.ac.uk/main.html REFMAC program data extraction PDB sw-help@rcsb.rutgers.edu April. 3, 2006 C++ http://pdb.rutgers.edu/software/ PDB_EXTRACT package 2.000 data collection ADSC Quantum data reduction HKL-2000 phasing SHELXD model building SHELXE Tumor necrosis factor ligand superfamily member 18 Crystal Structure of human GITRL 1 N N 2 N N The biological unit is a trimer disulf 2.025 A CYS 58 A SG CYS 11 1_555 A CYS 78 A SG CYS 31 1_555 SIGNALING PROTEIN GITRL; Glucocorticoid-Induced TNF Receptor Ligand, SIGNALING PROTEIN A GLY 63 A GLY 16 1 A PRO 64 A PRO 17 -2.15 A LEU 65 A LEU 18 1 A PRO 66 A PRO 19 4.77 A GLU 75 A GLU 28 1 A PRO 76 A PRO 29 -0.54 A GLU 75 A GLU 28 1 A PRO 76 A PRO 29 -2.66 TNF18_HUMAN UNP 1 52 Q9UNG2 ETAKEPCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTLTNKS KIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLANPQFIS 52 177 2Q1M 52 177 Q9UNG2 A 1 5 130 1 EXPRESSION TAG GLY 48 2Q1M A Q9UNG2 UNP 1 1 EXPRESSION TAG SER 49 2Q1M A Q9UNG2 UNP 2 1 EXPRESSION TAG HIS 50 2Q1M A Q9UNG2 UNP 3 1 EXPRESSION TAG MET 51 2Q1M A Q9UNG2 UNP 4 5 5 5 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TRP 69 A TRP 22 A ALA 72 A ALA 25 A MET 59 A MET 12 A PHE 62 A PHE 15 A TYR 164 A TYR 117 A ALA 171 A ALA 124 A GLY 93 A GLY 46 A VAL 101 A VAL 54 A GLN 134 A GLN 87 A ASN 135 A ASN 88 A TRP 69 A TRP 22 A ALA 72 A ALA 25 A MET 59 A MET 12 A PHE 62 A PHE 15 A TYR 164 A TYR 117 A ALA 171 A ALA 124 A GLY 93 A GLY 46 A VAL 101 A VAL 54 A GLY 138 A GLY 91 A LEU 142 A LEU 95 A VAL 79 A VAL 32 A SER 83 A SER 36 A LYS 86 A LYS 39 A ILE 89 A ILE 42 A THR 147 A THR 100 A PHE 152 A PHE 105 A VAL 115 A VAL 68 A LYS 119 A LYS 72 A ASP 122 A ASP 75 A LEU 127 A LEU 80 173 P 63