0.018896 0.010909 0.000000 0.000000 0.021819 0.000000 0.000000 0.000000 0.009776 0.00000 0.00000 0.00000 Filippova, E.V. Minasov, G. Shuvalova, L. Kiryukhina, O. Cobb, G. Joachimiak, A. Anderson, W.F. Midwest Center for Structural Genomics (MCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 52.922 52.922 102.295 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 Cl -1 35.453 CHLORIDE ION non-polymer 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 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 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 To be Published 0353 Crystal Structure of a Putative Endonuclease-Like Protein (Ngo0050) from Neisseria Gonorrhoeae 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 MIRROR CCD 2009-05-29 SI-111 CHANNEL SINGLE WAVELENGTH M x-ray 1 0.97872 1.0 21-ID-F APS 0.97872 0.97872 SYNCHROTRON APS BEAMLINE 21-ID-F 12215.399 Endonuclease-Like Protein 1 man polymer 35.453 CHLORIDE ION 1 syn non-polymer 18.015 water 105 nat water no yes SNA(MSE)SEAEAKLWQHLRAGRLNGYKFRRQQP(MSE)GNYIVDF(MSE)CVTPKLIVEADGGQHAEQAVYDHARTVYL NSLGFTVLRFWNHEILQQTNDVLAEILRVLQELEKQ SNAMSEAEAKLWQHLRAGRLNGYKFRRQQPMGNYIVDFMCVTPKLIVEADGGQHAEQAVYDHARTVYLNSLGFTVLRFWN HEILQQTNDVLAEILRVLQELEKQ A apc63439.1 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 sample NGO0050 242231 Neisseria gonorrhoeae FA 1090 511693 Escherichia coli BL21 BL21magic PLASMID pMCSG7 1 3.39 63.67 VAPOR DIFFUSION, HANGING DROP 7.0 3M NaCl, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K 294 Midwest Center for Structural Genomics MCSG PSI, Protein Structure Initiative software repository Initial release Advisory Version format compliance Refinement description 1 0 2009-06-30 1 1 2011-07-13 1 2 2017-11-01 _software.name Y RCSB Y RCSB 2009-06-09 REL REL CL CHLORIDE ION HOH water CL 1 2 CL CL 1 A HOH 2 3 HOH HOH 2 A HOH 3 3 HOH HOH 3 A HOH 4 3 HOH HOH 4 A HOH 5 3 HOH HOH 5 A HOH 6 3 HOH HOH 6 A HOH 7 3 HOH HOH 7 A HOH 8 3 HOH HOH 8 A HOH 9 3 HOH HOH 9 A HOH 10 3 HOH HOH 10 A HOH 11 3 HOH HOH 11 A HOH 12 3 HOH HOH 12 A HOH 13 3 HOH HOH 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 127 A HOH 27 3 HOH HOH 128 A HOH 28 3 HOH HOH 129 A HOH 29 3 HOH HOH 130 A HOH 30 3 HOH HOH 131 A HOH 31 3 HOH HOH 132 A HOH 32 3 HOH HOH 133 A HOH 33 3 HOH HOH 134 A HOH 34 3 HOH HOH 135 A HOH 35 3 HOH HOH 136 A HOH 36 3 HOH HOH 137 A HOH 37 3 HOH HOH 138 A HOH 38 3 HOH HOH 139 A HOH 39 3 HOH HOH 140 A HOH 40 3 HOH HOH 141 A HOH 41 3 HOH HOH 142 A HOH 42 3 HOH HOH 143 A HOH 43 3 HOH HOH 144 A HOH 44 3 HOH HOH 145 A HOH 45 3 HOH HOH 146 A HOH 46 3 HOH HOH 147 A HOH 47 3 HOH HOH 148 A HOH 48 3 HOH HOH 149 A HOH 49 3 HOH HOH 150 A HOH 50 3 HOH HOH 151 A HOH 51 3 HOH HOH 152 A HOH 52 3 HOH HOH 153 A HOH 53 3 HOH HOH 154 A HOH 54 3 HOH HOH 155 A HOH 55 3 HOH HOH 156 A HOH 56 3 HOH HOH 157 A HOH 57 3 HOH HOH 158 A HOH 58 3 HOH HOH 159 A HOH 59 3 HOH HOH 160 A HOH 60 3 HOH HOH 161 A HOH 61 3 HOH HOH 162 A HOH 62 3 HOH HOH 163 A HOH 63 3 HOH HOH 164 A HOH 64 3 HOH HOH 165 A HOH 65 3 HOH HOH 166 A HOH 66 3 HOH HOH 167 A HOH 67 3 HOH HOH 168 A HOH 68 3 HOH HOH 169 A HOH 69 3 HOH HOH 170 A HOH 70 3 HOH HOH 171 A HOH 71 3 HOH HOH 172 A HOH 72 3 HOH HOH 173 A HOH 73 3 HOH HOH 174 A HOH 74 3 HOH HOH 175 A HOH 75 3 HOH HOH 176 A HOH 76 3 HOH HOH 177 A HOH 77 3 HOH HOH 178 A HOH 78 3 HOH HOH 179 A HOH 79 3 HOH HOH 180 A HOH 80 3 HOH HOH 181 A HOH 81 3 HOH HOH 182 A HOH 82 3 HOH HOH 183 A HOH 83 3 HOH HOH 184 A HOH 84 3 HOH HOH 185 A HOH 85 3 HOH HOH 186 A HOH 86 3 HOH HOH 187 A HOH 87 3 HOH HOH 188 A HOH 88 3 HOH HOH 189 A HOH 89 3 HOH HOH 190 A HOH 90 3 HOH HOH 191 A HOH 91 3 HOH HOH 192 A HOH 92 3 HOH HOH 193 A HOH 93 3 HOH HOH 194 A HOH 94 3 HOH HOH 195 A HOH 95 3 HOH HOH 196 A HOH 96 3 HOH HOH 197 A HOH 97 3 HOH HOH 198 A HOH 98 3 HOH HOH 199 A HOH 99 3 HOH HOH 200 A HOH 100 3 HOH HOH 201 A HOH 101 3 HOH HOH 202 A HOH 102 3 HOH HOH 203 A HOH 103 3 HOH HOH 204 A HOH 104 3 HOH HOH 205 A HOH 105 3 HOH HOH 206 A HOH 106 3 HOH HOH 207 A n 1 -2 A n 2 -1 A ALA 0 n 3 ALA 0 A MSE 26 n 4 MSE 26 A SER 27 n 5 SER 27 A GLU 28 n 6 GLU 28 A ALA 29 n 7 ALA 29 A GLU 30 n 8 GLU 30 A ALA 31 n 9 ALA 31 A LYS 32 n 10 LYS 32 A LEU 33 n 11 LEU 33 A TRP 34 n 12 TRP 34 A GLN 35 n 13 GLN 35 A HIS 36 n 14 HIS 36 A LEU 37 n 15 LEU 37 A ARG 38 n 16 ARG 38 A ALA 39 n 17 ALA 39 A GLY 40 n 18 GLY 40 A ARG 41 n 19 ARG 41 A LEU 42 n 20 LEU 42 A ASN 43 n 21 ASN 43 A GLY 44 n 22 GLY 44 A TYR 45 n 23 TYR 45 A LYS 46 n 24 LYS 46 A PHE 47 n 25 PHE 47 A ARG 48 n 26 ARG 48 A ARG 49 n 27 ARG 49 A GLN 50 n 28 GLN 50 A GLN 51 n 29 GLN 51 A PRO 52 n 30 PRO 52 A MSE 53 n 31 MSE 53 A GLY 54 n 32 GLY 54 A ASN 55 n 33 ASN 55 A TYR 56 n 34 TYR 56 A ILE 57 n 35 ILE 57 A VAL 58 n 36 VAL 58 A ASP 59 n 37 ASP 59 A PHE 60 n 38 PHE 60 A MSE 61 n 39 MSE 61 A CYS 62 n 40 CYS 62 A VAL 63 n 41 VAL 63 A THR 64 n 42 THR 64 A PRO 65 n 43 PRO 65 A LYS 66 n 44 LYS 66 A LEU 67 n 45 LEU 67 A ILE 68 n 46 ILE 68 A VAL 69 n 47 VAL 69 A GLU 70 n 48 GLU 70 A ALA 71 n 49 ALA 71 A ASP 72 n 50 ASP 72 A GLY 73 n 51 GLY 73 A n 52 74 A n 53 75 A n 54 76 A n 55 77 A n 56 78 A n 57 79 A n 58 80 A VAL 81 n 59 VAL 81 A TYR 82 n 60 TYR 82 A ASP 83 n 61 ASP 83 A HIS 84 n 62 HIS 84 A ALA 85 n 63 ALA 85 A ARG 86 n 64 ARG 86 A THR 87 n 65 THR 87 A VAL 88 n 66 VAL 88 A TYR 89 n 67 TYR 89 A LEU 90 n 68 LEU 90 A ASN 91 n 69 ASN 91 A SER 92 n 70 SER 92 A LEU 93 n 71 LEU 93 A GLY 94 n 72 GLY 94 A PHE 95 n 73 PHE 95 A THR 96 n 74 THR 96 A VAL 97 n 75 VAL 97 A LEU 98 n 76 LEU 98 A ARG 99 n 77 ARG 99 A PHE 100 n 78 PHE 100 A TRP 101 n 79 TRP 101 A ASN 102 n 80 ASN 102 A HIS 103 n 81 HIS 103 A GLU 104 n 82 GLU 104 A ILE 105 n 83 ILE 105 A LEU 106 n 84 LEU 106 A GLN 107 n 85 GLN 107 A GLN 108 n 86 GLN 108 A THR 109 n 87 THR 109 A ASN 110 n 88 ASN 110 A ASP 111 n 89 ASP 111 A VAL 112 n 90 VAL 112 A LEU 113 n 91 LEU 113 A ALA 114 n 92 ALA 114 A GLU 115 n 93 GLU 115 A ILE 116 n 94 ILE 116 A LEU 117 n 95 LEU 117 A ARG 118 n 96 ARG 118 A VAL 119 n 97 VAL 119 A LEU 120 n 98 LEU 120 A GLN 121 n 99 GLN 121 A GLU 122 n 100 GLU 122 A LEU 123 n 101 LEU 123 A GLU 124 n 102 GLU 124 A LYS 125 n 103 LYS 125 A n 104 126 A 2.8971 0.5420 0.9626 0.9887 0.4558 1.4877 -0.0131 0.1571 -0.0196 -0.0458 0.0904 0.0156 -0.0181 0.0068 -0.0773 0.0517 0.0085 0.0086 0.0852 0.0165 0.0103 refined 34.4501 22.4862 20.4432 X-RAY DIFFRACTION A 26 A 125 X-RAY DIFFRACTION 1 author_and_software_defined_assembly PISA 1 monomeric A MSE 26 SELENOMETHIONINE A MSE 4 MET A MSE 53 SELENOMETHIONINE A MSE 31 MET A MSE 61 SELENOMETHIONINE A MSE 39 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 A N MSE 53 A N MSE 31 A O TYR 56 A O TYR 34 A N CYS 62 A N CYS 40 A O LEU 67 A O LEU 45 A N ASP 72 A N ASP 50 A O PHE 100 A O PHE 78 1 A SER -2 A SER 1 1 Y 1 A ASN -1 A ASN 2 1 Y 1 A GLY 74 A GLY 52 1 Y 1 A GLN 75 A GLN 53 1 Y 1 A HIS 76 A HIS 54 1 Y 1 A ALA 77 A ALA 55 1 Y 1 A GLU 78 A GLU 56 1 Y 1 A GLN 79 A GLN 57 1 Y 1 A ALA 80 A ALA 58 1 Y 1 A GLN 126 A GLN 104 1 Y 19.925 1.65 0.82 0.00 1.65 0.00 -2.47 0.957 0.943 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.22600 0.18316 0.18521 1.95 22.33 604 12588 11984 4.8 99.83 5.694 0.077 RANDOM LIKELY RESIDUAL 1 THROUGHOUT SAD 0.117 0.122 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 1.95 22.33 105 881 1 0 775 0.019 0.022 790 0.001 0.020 539 1.615 1.941 1066 0.901 3.000 1301 5.733 5.000 92 28.800 23.571 42 12.223 15.000 141 12.846 15.000 7 0.098 0.200 117 0.007 0.020 867 0.001 0.020 170 1.087 1.500 465 0.314 1.500 190 1.997 2.000 746 3.529 3.000 325 5.930 4.500 320 0.265 0.190 2.001 37 839 20 98.65 1.950 22.330 3HRL 23330 23330 -3.000 0.07000 0.07000 1 21.7120 5.800 99.9 0.35300 1.95 1.98 5.200 0.35300 1 5.80 98.7 data collection Blu-Ice Max phasing HKL-3000 phasing MLPHARE model building DM phasing SHELXD model building ARP/wARP model building Coot refinement REFMAC 5.5.0051 data reduction HKL-2000 data scaling HKL-2000 phasing DM Endonuclease-Like Protein Crystal structure of a putative endonuclease-like protein (ngo0050) from neisseria gonorrhoeae 1 N N 2 N N 3 N N A SER 27 A SER 5 HELX_P A ARG 38 A ARG 16 1 1 12 A ALA 39 A ALA 17 HELX_P A ARG 41 A ARG 19 5 2 3 A ASP 83 A ASP 61 HELX_P A LEU 93 A LEU 71 1 3 11 A ASN 102 A ASN 80 HELX_P A GLN 108 A GLN 86 1 4 7 A GLN 108 A GLN 86 HELX_P A LYS 125 A LYS 103 1 5 18 covale 1.332 A ALA 0 A C ALA 3 1_555 A MSE 26 A N MSE 4 1_555 covale 1.327 A MSE 26 A C MSE 4 1_555 A SER 27 A N SER 5 1_555 covale 1.325 A PRO 52 A C PRO 30 1_555 A MSE 53 A N MSE 31 1_555 covale 1.322 A MSE 53 A C MSE 31 1_555 A GLY 54 A N GLY 32 1_555 covale 1.330 A PHE 60 A C PHE 38 1_555 A MSE 61 A N MSE 39 1_555 covale 1.323 A MSE 61 A C MSE 39 1_555 A CYS 62 A N CYS 40 1_555 structural genomics, unknown function STRUCTURAL GENOMICS; ENDONUCLEASE; NEISSERIA GONORRHOEAE, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, structural genomics, unknown function A THR 64 A THR 42 1 A PRO 65 A PRO 43 -3.69 Q5FAH0_NEIG1 UNP 1 27 Q5FAH0 SEAEAKLWQHLRAGRLNGYKFRRQQPMGNYIVDFMCVTPKLIVEADGGQHAEQAVYDHARTVYLNSLGFTVLRFWNHEIL QQTNDVLAEILRVLQELEKQ 27 126 3HRL 27 126 Q5FAH0 A 1 5 104 1 expression tag SER -2 3HRL A Q5FAH0 UNP 1 1 expression tag ASN -1 3HRL A Q5FAH0 UNP 2 1 expression tag ALA 0 3HRL A Q5FAH0 UNP 3 1 expression tag MSE 26 3HRL A Q5FAH0 UNP 4 4 anti-parallel anti-parallel parallel A PHE 47 A PHE 25 A MSE 53 A MSE 31 A TYR 56 A TYR 34 A CYS 62 A CYS 40 A LEU 67 A LEU 45 A ASP 72 A ASP 50 A THR 96 A THR 74 A TRP 101 A TRP 79 BINDING SITE FOR RESIDUE CL A 1 Software 4 A TYR 56 A TYR 34 4 1_555 A ILE 57 A ILE 35 4 1_555 A ARG 86 A ARG 64 4 1_555 A HOH 146 C HOH 4 1_555 154 P 32 2 1