0.013158 0.007597 0.000000 0.000000 0.015193 0.000000 0.000000 0.000000 0.023263 0.00000 0.00000 0.00000 Chruszcz, M. Evdokimova, E. Cymborowski, M. Kagan, O. Savchenko, A. Edwards, A. Joachimiak, A. 0000-0001-7075-7090 Minor, W. Midwest Center for Structural Genomics (MCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 76.000 76.000 42.987 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 S 149.211 y METHIONINE 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 UK Evol Appl 1752-4571 6 434 449 10.1111/eva.12057 23745136 Structural and functional insight into the universal stress protein family. 2013 0000-0001-7075-7090 10.2210/pdb2pfs/pdb pdb_00002pfs 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 1 Mirrors CCD 2007-02-08 ADSC QUANTUM 315 Si 111 CHANNEL SINGLE WAVELENGTH M x-ray 1 0.97918 1.0 19-ID APS 0.97918 SYNCHROTRON APS BEAMLINE 19-ID 16756.553 Universal stress protein 1 man polymer 35.453 CHLORIDE ION 2 syn non-polymer 18.015 water 40 nat water Usp no yes GH(MSE)SVYHHILLAVDFSSEDSQVVQKVRNLASQIGARLSLIHVLDNIP(MSE)PDTPYGTAIPLDTETTYDA(MSE) LDVEKQKLSQIGNTLGIDPAHRWLVWGEPREEIIRIAEQENVDLIVVGSHGRHGLALLLGSTANSVLHYAKCDVLAVRLR DD GHMSVYHHILLAVDFSSEDSQVVQKVRNLASQIGARLSLIHVLDNIPMPDTPYGTAIPLDTETTYDAMLDVEKQKLSQIG NTLGIDPAHRWLVWGEPREEIIRIAEQENVDLIVVGSHGRHGLALLLGSTANSVLHYAKCDVLAVRLRDD A APC6354 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 n n n n n n n n n n n n n n n n n n n n Nitrosomonas Nitrosomonas europaea IFO 14298 Escherichia sample NE1028 228410 Nitrosomonas europaea ATCC 19718 562 Escherichia coli BL21-Gold(DE3) plasmid p15TV-L 1 2.14 42.47 VAPOR DIFFUSION 7.5 0.2M Sodium chloride, 0.1M HEPES pH 7.5, 25% PEG3350, 2% Isopropanol, VAPOR DIFFUSION, temperature 293K 293 Midwest Center for Structural Genomics MCSG PSI, Protein Structure Initiative audit_author citation_author database_2 struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Advisory Version format compliance Derived calculations Database references Database references Database references Derived calculations Structure summary 1 0 2007-05-08 1 1 2008-05-01 1 2 2011-07-13 1 3 2011-09-14 1 4 2013-04-17 1 5 2013-06-26 1 6 2022-04-13 _audit_author.identifier_ORCID _citation_author.identifier_ORCID _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y RCSB Y RCSB 2007-04-05 REL REL CL CHLORIDE ION HOH water CL 1 2 CL CL 149 A CL 1 2 CL CL 150 A HOH 4 3 HOH HOH 151 A HOH 6 3 HOH HOH 152 A HOH 8 3 HOH HOH 153 A HOH 10 3 HOH HOH 154 A HOH 11 3 HOH HOH 155 A HOH 12 3 HOH HOH 156 A HOH 14 3 HOH HOH 157 A HOH 15 3 HOH HOH 158 A HOH 18 3 HOH HOH 159 A HOH 19 3 HOH HOH 160 A HOH 20 3 HOH HOH 161 A HOH 25 3 HOH HOH 162 A HOH 30 3 HOH HOH 163 A HOH 31 3 HOH HOH 164 A HOH 33 3 HOH HOH 165 A HOH 34 3 HOH HOH 166 A HOH 38 3 HOH HOH 167 A HOH 50 3 HOH HOH 168 A HOH 56 3 HOH HOH 169 A HOH 57 3 HOH HOH 170 A HOH 59 3 HOH HOH 171 A HOH 60 3 HOH HOH 172 A HOH 63 3 HOH HOH 173 A HOH 64 3 HOH HOH 174 A HOH 65 3 HOH HOH 175 A HOH 66 3 HOH HOH 176 A HOH 67 3 HOH HOH 177 A HOH 68 3 HOH HOH 178 A HOH 70 3 HOH HOH 179 A HOH 71 3 HOH HOH 180 A HOH 72 3 HOH HOH 181 A HOH 73 3 HOH HOH 182 A HOH 74 3 HOH HOH 183 A HOH 75 3 HOH HOH 184 A HOH 76 3 HOH HOH 185 A HOH 2 3 HOH HOH 186 A HOH 3 3 HOH HOH 187 A HOH 4 3 HOH HOH 188 A HOH 6 3 HOH HOH 189 A HOH 7 3 HOH HOH 190 A n 1 -1 A n 2 0 A MSE 1 n 3 MSE 1 A SER 2 n 4 SER 2 A VAL 3 n 5 VAL 3 A TYR 4 n 6 TYR 4 A HIS 5 n 7 HIS 5 A HIS 6 n 8 HIS 6 A ILE 7 n 9 ILE 7 A LEU 8 n 10 LEU 8 A LEU 9 n 11 LEU 9 A ALA 10 n 12 ALA 10 A VAL 11 n 13 VAL 11 A ASP 12 n 14 ASP 12 A PHE 13 n 15 PHE 13 A SER 14 n 16 SER 14 A SER 15 n 17 SER 15 A GLU 16 n 18 GLU 16 A ASP 17 n 19 ASP 17 A SER 18 n 20 SER 18 A GLN 19 n 21 GLN 19 A VAL 20 n 22 VAL 20 A VAL 21 n 23 VAL 21 A GLN 22 n 24 GLN 22 A LYS 23 n 25 LYS 23 A VAL 24 n 26 VAL 24 A ARG 25 n 27 ARG 25 A ASN 26 n 28 ASN 26 A LEU 27 n 29 LEU 27 A ALA 28 n 30 ALA 28 A SER 29 n 31 SER 29 A GLN 30 n 32 GLN 30 A ILE 31 n 33 ILE 31 A GLY 32 n 34 GLY 32 A ALA 33 n 35 ALA 33 A ARG 34 n 36 ARG 34 A LEU 35 n 37 LEU 35 A SER 36 n 38 SER 36 A LEU 37 n 39 LEU 37 A ILE 38 n 40 ILE 38 A HIS 39 n 41 HIS 39 A VAL 40 n 42 VAL 40 A LEU 41 n 43 LEU 41 A ASP 42 n 44 ASP 42 A n 45 43 A n 46 44 A n 47 45 A n 48 46 A n 49 47 A n 50 48 A n 51 49 A n 52 50 A n 53 51 A n 54 52 A THR 53 n 55 THR 53 A ALA 54 n 56 ALA 54 A ILE 55 n 57 ILE 55 A PRO 56 n 58 PRO 56 A LEU 57 n 59 LEU 57 A ASP 58 n 60 ASP 58 A THR 59 n 61 THR 59 A GLU 60 n 62 GLU 60 A THR 61 n 63 THR 61 A THR 62 n 64 THR 62 A TYR 63 n 65 TYR 63 A ASP 64 n 66 ASP 64 A ALA 65 n 67 ALA 65 A MSE 66 n 68 MSE 66 A LEU 67 n 69 LEU 67 A ASP 68 n 70 ASP 68 A VAL 69 n 71 VAL 69 A GLU 70 n 72 GLU 70 A LYS 71 n 73 LYS 71 A GLN 72 n 74 GLN 72 A LYS 73 n 75 LYS 73 A LEU 74 n 76 LEU 74 A SER 75 n 77 SER 75 A GLN 76 n 78 GLN 76 A ILE 77 n 79 ILE 77 A GLY 78 n 80 GLY 78 A ASN 79 n 81 ASN 79 A THR 80 n 82 THR 80 A LEU 81 n 83 LEU 81 A GLY 82 n 84 GLY 82 A ILE 83 n 85 ILE 83 A ASP 84 n 86 ASP 84 A PRO 85 n 87 PRO 85 A ALA 86 n 88 ALA 86 A HIS 87 n 89 HIS 87 A ARG 88 n 90 ARG 88 A TRP 89 n 91 TRP 89 A LEU 90 n 92 LEU 90 A VAL 91 n 93 VAL 91 A TRP 92 n 94 TRP 92 A GLY 93 n 95 GLY 93 A GLU 94 n 96 GLU 94 A PRO 95 n 97 PRO 95 A ARG 96 n 98 ARG 96 A GLU 97 n 99 GLU 97 A GLU 98 n 100 GLU 98 A ILE 99 n 101 ILE 99 A ILE 100 n 102 ILE 100 A ARG 101 n 103 ARG 101 A ILE 102 n 104 ILE 102 A ALA 103 n 105 ALA 103 A GLU 104 n 106 GLU 104 A GLN 105 n 107 GLN 105 A GLU 106 n 108 GLU 106 A ASN 107 n 109 ASN 107 A VAL 108 n 110 VAL 108 A ASP 109 n 111 ASP 109 A LEU 110 n 112 LEU 110 A ILE 111 n 113 ILE 111 A VAL 112 n 114 VAL 112 A VAL 113 n 115 VAL 113 A GLY 114 n 116 GLY 114 A SER 115 n 117 SER 115 A HIS 116 n 118 HIS 116 A n 119 117 A n 120 118 A n 121 119 A n 122 120 A n 123 121 A n 124 122 A n 125 123 A n 126 124 A n 127 125 A n 128 126 A SER 127 n 129 SER 127 A THR 128 n 130 THR 128 A ALA 129 n 131 ALA 129 A ASN 130 n 132 ASN 130 A SER 131 n 133 SER 131 A VAL 132 n 134 VAL 132 A LEU 133 n 135 LEU 133 A HIS 134 n 136 HIS 134 A TYR 135 n 137 TYR 135 A ALA 136 n 138 ALA 136 A LYS 137 n 139 LYS 137 A CYS 138 n 140 CYS 138 A ASP 139 n 141 ASP 139 A VAL 140 n 142 VAL 140 A LEU 141 n 143 LEU 141 A ALA 142 n 144 ALA 142 A VAL 143 n 145 VAL 143 A ARG 144 n 146 ARG 144 A LEU 145 n 147 LEU 145 A n 148 146 A n 149 147 A n 150 148 A 11.9458 -4.8695 3.5244 3.9491 -0.7759 1.2621 0.0194 -0.8252 -1.0076 -0.1127 0.1368 0.3162 0.1841 -0.1601 -0.1563 -0.1725 -0.0089 0.0133 -0.1242 0.0155 -0.0816 refined 5.8857 28.9971 17.1948 X-RAY DIFFRACTION 10.0510 -3.2718 0.2266 5.7113 -1.4397 2.5845 -0.1434 -0.2108 0.3651 -0.0489 0.1067 -0.1207 0.0229 0.0051 0.0367 -0.1645 0.0442 0.0230 -0.1822 -0.0286 -0.1777 refined 11.8603 34.7075 18.2779 X-RAY DIFFRACTION 10.0661 3.0639 7.5595 0.9326 2.3009 5.6770 1.1132 -0.7862 -0.5534 0.2488 -0.1528 -0.1619 0.7903 -0.8214 -0.9604 0.1747 -0.0976 -0.2199 0.3257 -0.1174 0.3420 refined -13.6798 23.1851 5.0710 X-RAY DIFFRACTION 6.8401 -1.1359 3.0985 0.1887 -0.5196 2.7848 0.3721 0.2271 -1.3816 -0.4396 0.0875 0.2890 0.5125 -0.0443 -0.4596 0.0376 -0.0013 -0.0362 -0.0799 -0.0870 0.1385 refined 1.3176 25.9613 10.4891 X-RAY DIFFRACTION A 2 A 4 A 20 A 22 X-RAY DIFFRACTION 1 A 21 A 23 A 35 A 37 X-RAY DIFFRACTION 2 A 36 A 38 A 60 A 62 X-RAY DIFFRACTION 3 A 61 A 63 A 145 A 147 X-RAY DIFFRACTION 4 author_and_software_defined_assembly PISA 2 dimeric 2140 -52 12930 A MSE 1 SELENOMETHIONINE A MSE 3 MET A MSE 66 SELENOMETHIONINE A MSE 68 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 4_556 y,x,-z+1 crystal symmetry operation 0.0000000000 0.0000000000 42.9870000000 A O VAL 91 A O VAL 93 A N LEU 41 A N LEU 43 A O ARG 34 A O ARG 36 A N ILE 7 A N ILE 9 A N LEU 8 A N LEU 10 A O LEU 110 A O LEU 112 A N VAL 113 A N VAL 115 A O VAL 143 A O VAL 145 1 A CG MSE 1 A CG MSE 3 1 Y 1 A SE MSE 1 A SE MSE 3 1 Y 1 A CE MSE 1 A CE MSE 3 1 Y 1 A CG GLU 94 A CG GLU 96 1 Y 1 A CD GLU 94 A CD GLU 96 1 Y 1 A OE1 GLU 94 A OE1 GLU 96 1 Y 1 A OE2 GLU 94 A OE2 GLU 96 1 Y 1 A CG ARG 96 A CG ARG 98 1 Y 1 A CD ARG 96 A CD ARG 98 1 Y 1 A NE ARG 96 A NE ARG 98 1 Y 1 A CZ ARG 96 A CZ ARG 98 1 Y 1 A NH1 ARG 96 A NH1 ARG 98 1 Y 1 A NH2 ARG 96 A NH2 ARG 98 1 Y 1 A CG GLU 104 A CG GLU 106 1 Y 1 A CD GLU 104 A CD GLU 106 1 Y 1 A OE1 GLU 104 A OE1 GLU 106 1 Y 1 A OE2 GLU 104 A OE2 GLU 106 1 Y 1 A OG SER 127 A OG SER 129 1 Y 1 A CG ASN 130 A CG ASN 132 1 Y 1 A OD1 ASN 130 A OD1 ASN 132 1 Y 1 A ND2 ASN 130 A ND2 ASN 132 1 Y 1 A OG SER 131 A OG SER 133 1 Y 1 A CG HIS 134 A CG HIS 136 1 Y 1 A ND1 HIS 134 A ND1 HIS 136 1 Y 1 A CD2 HIS 134 A CD2 HIS 136 1 Y 1 A CE1 HIS 134 A CE1 HIS 136 1 Y 1 A NE2 HIS 134 A NE2 HIS 136 1 Y 1 A CG TYR 135 A CG TYR 137 1 Y 1 A CD1 TYR 135 A CD1 TYR 137 1 Y 1 A CD2 TYR 135 A CD2 TYR 137 1 Y 1 A CE1 TYR 135 A CE1 TYR 137 1 Y 1 A CE2 TYR 135 A CE2 TYR 137 1 Y 1 A CZ TYR 135 A CZ TYR 137 1 Y 1 A OH TYR 135 A OH TYR 137 1 Y 1 A CG LYS 137 A CG LYS 139 1 Y 1 A CD LYS 137 A CD LYS 139 1 Y 1 A CE LYS 137 A CE LYS 139 1 Y 1 A NZ LYS 137 A NZ LYS 139 1 Y 1 A CG ARG 144 A CG ARG 146 1 Y 1 A CD ARG 144 A CD ARG 146 1 Y 1 A NE ARG 144 A NE ARG 146 1 Y 1 A CZ ARG 144 A CZ ARG 146 1 Y 1 A NH1 ARG 144 A NH1 ARG 146 1 Y 1 A NH2 ARG 144 A NH2 ARG 146 1 Y 1 A GLY -1 A GLY 1 1 Y 1 A HIS 0 A HIS 2 1 Y 1 A ASN 43 A ASN 45 1 Y 1 A ILE 44 A ILE 46 1 Y 1 A PRO 45 A PRO 47 1 Y 1 A MSE 46 A MSE 48 1 Y 1 A PRO 47 A PRO 49 1 Y 1 A ASP 48 A ASP 50 1 Y 1 A THR 49 A THR 51 1 Y 1 A PRO 50 A PRO 52 1 Y 1 A TYR 51 A TYR 53 1 Y 1 A GLY 52 A GLY 54 1 Y 1 A GLY 117 A GLY 119 1 Y 1 A ARG 118 A ARG 120 1 Y 1 A HIS 119 A HIS 121 1 Y 1 A GLY 120 A GLY 122 1 Y 1 A LEU 121 A LEU 123 1 Y 1 A ALA 122 A ALA 124 1 Y 1 A LEU 123 A LEU 125 1 Y 1 A LEU 124 A LEU 126 1 Y 1 A LEU 125 A LEU 127 1 Y 1 A GLY 126 A GLY 128 1 Y 1 A ARG 146 A ARG 148 1 Y 1 A ASP 147 A ASP 149 1 Y 1 A ASP 148 A ASP 150 1 Y 1 A A SER HIS 115 116 56.94 52.420 -1.80 -0.90 0.00 -1.80 0.00 2.70 0.951 0.927 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.25455 0.19471 0.19758 0.19758 2.25 50.00 329 6538 6538 4.8 97.57 11.231 0.141 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0 0 SAD 0.277 0.228 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 2.25 50.00 40 978 2 0 936 0.017 0.021 957 1.563 1.953 1308 8.463 5.000 124 38.880 25.263 38 13.601 15.000 154 13.282 15.000 4 0.113 0.200 167 0.006 0.020 697 0.214 0.200 397 0.302 0.200 669 0.136 0.200 51 0.211 0.200 33 0.254 0.200 11 1.182 1.500 647 1.740 2.000 1006 2.736 3.000 352 4.252 4.500 302 0.229 0.199 2.309 20 407 20 83.07 2.25 50.0 2PFS 6882 6882 0 -3 0.06 0.06 1 58.5 11.1 97.6 0.486 2.25 2.29 2.9 277 0.486 1 7.7 81.5 refinement REFMAC 5.2.0005 data collection HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing HKL-3000 phasing SHELXD model building SHELXE phasing CCP4 phasing MLPHARE phasing DM model building O model building Coot phasing SOLVE phasing RESOLVE model building ARP/wARP Crystal structure of universal stress protein from Nitrosomonas europaea 1 N N 2 N N 2 N N 3 N N A GLU 16 A GLU 18 HELX_P A GLY 32 A GLY 34 1 1 17 A THR 62 A THR 64 HELX_P A GLY 82 A GLY 84 1 2 21 A ASP 84 A ASP 86 HELX_P A ALA 86 A ALA 88 5 3 3 A GLU 94 A GLU 96 HELX_P A GLU 106 A GLU 108 1 4 13 A SER 127 A SER 129 HELX_P A ALA 136 A ALA 138 1 5 10 covale 1.327 both A MSE 1 A C MSE 3 1_555 A SER 2 A N SER 4 1_555 covale 1.346 both A ALA 65 A C ALA 67 1_555 A MSE 66 A N MSE 68 1_555 covale 1.331 both A MSE 66 A C MSE 68 1_555 A LEU 67 A N LEU 69 1_555 STRUCTURAL GENOMICS, UNKNOWN FUNCTION stress protein, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION A LEU 41 A LEU 43 1 A ASP 42 A ASP 44 22.48 Q82VN8_NITEU UNP 1 1 Q82VN8 MSVYHHILLAVDFSSEDSQVVQKVRNLASQIGARLSLIHVLDNIPMPDTPYGTAIPLDTETTYDAMLDVEKQKLSQIGNT LGIDPAHRWLVWGEPREEIIRIAEQENVDLIVVGSHGRHGLALLLGSTANSVLHYAKCDVLAVRLRDD 1 148 2PFS 1 148 Q82VN8 A 1 3 150 1 cloning artifact GLY -1 2PFS A Q82VN8 UNP 1 1 cloning artifact HIS 0 2PFS A Q82VN8 UNP 2 1 MET modified residue MSE 1 2PFS A Q82VN8 UNP 1 3 1 MET modified residue MSE 46 2PFS A Q82VN8 UNP 46 48 1 MET modified residue MSE 66 2PFS A Q82VN8 UNP 66 68 5 parallel parallel parallel parallel A ARG 88 A ARG 90 A TRP 92 A TRP 94 A ARG 34 A ARG 36 A LEU 41 A LEU 43 A HIS 6 A HIS 8 A ALA 10 A ALA 12 A LEU 110 A LEU 112 A SER 115 A SER 117 A ASP 139 A ASP 141 A ARG 144 A ARG 146 BINDING SITE FOR RESIDUE CL A 149 A CL 149 Software 2 BINDING SITE FOR RESIDUE CL A 150 A CL 150 Software 1 A VAL 11 A VAL 13 2 1_555 A VAL 40 A VAL 42 2 1_555 A THR 62 A THR 64 1 1_555 150 P 3 2 1