0.019818 0.000000 0.008482 -0.000000 0.040420 0.000000 0.000000 -0.000000 0.022828 0.00000 0.00000 0.00000 Huguenin-Dezot, N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 113.17 90.00 50.460 24.740 47.650 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 S 149.211 y METHIONINE L-peptide linking C4 H10 O3 106.120 DI(HYDROXYETHYL)ETHER non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking O4 P -3 94.971 PHOSPHATE ION non-polymer 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 C4 H10 N O6 P 199.099 n PHOSPHOTHREONINE PHOSPHONOTHREONINE 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 Nat. Methods 1548-7105 14 729 736 10.1038/nmeth.4302 28553966 Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing. 2017 100 1 PIXEL 2017-03-04 DECTRIS PILATUS3 6M SINGLE WAVELENGTH M x-ray 1 0.97199 1.0 ID23-1 ESRF 0.97199 SYNCHROTRON ESRF BEAMLINE ID23-1 8656.811 Polyubiquitin-B 1 man polymer 94.971 PHOSPHATE ION 1 syn non-polymer 106.120 DI(HYDROXYETHYL)ETHER 1 syn non-polymer 18.015 water 62 nat water no yes MQIFVKTLTGK(TPO)ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 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 Human sample 1 76 UBB 9606 Homo sapiens 562 Escherichia coli Biological sequence 1 1.58 22.12 VAPOR DIFFUSION, SITTING DROP 4.2 20% (v/v) ethanol, 20% (w/v) PEG-1000, 0.1M Phosphate-citrate pH 4.2 291.15 citation pdbx_audit_support repository Initial release Database references Database references Author supporting evidence 1 0 2017-05-31 1 1 2017-06-07 1 2 2017-07-12 1 3 2017-09-13 _citation.country _citation.journal_volume _citation.page_first _citation.page_last _pdbx_audit_support.funding_organization United Kingdom Medical Research Council (United Kingdom) MC_U105181009 United Kingdom Medical Research Council (United Kingdom) MC_UP_A024_1008 N PDBE Y PDBE 2017-05-04 REL REL PO4 PHOSPHATE ION PEG DI(HYDROXYETHYL)ETHER HOH water PO4 1 2 PO4 PO4 101 A PEG 1 3 PEG PEG 102 A HOH 74 4 HOH HOH 201 A HOH 36 4 HOH HOH 202 A HOH 66 4 HOH HOH 203 A HOH 54 4 HOH HOH 204 A HOH 23 4 HOH HOH 205 A HOH 47 4 HOH HOH 206 A HOH 33 4 HOH HOH 207 A HOH 40 4 HOH HOH 208 A HOH 2 4 HOH HOH 209 A HOH 28 4 HOH HOH 210 A HOH 29 4 HOH HOH 211 A HOH 67 4 HOH HOH 212 A HOH 56 4 HOH HOH 213 A HOH 57 4 HOH HOH 214 A HOH 69 4 HOH HOH 215 A HOH 70 4 HOH HOH 216 A HOH 59 4 HOH HOH 217 A HOH 20 4 HOH HOH 218 A HOH 10 4 HOH HOH 219 A HOH 9 4 HOH HOH 220 A HOH 21 4 HOH HOH 221 A HOH 7 4 HOH HOH 222 A HOH 64 4 HOH HOH 223 A HOH 25 4 HOH HOH 224 A HOH 46 4 HOH HOH 225 A HOH 6 4 HOH HOH 226 A HOH 1 4 HOH HOH 227 A HOH 14 4 HOH HOH 228 A HOH 4 4 HOH HOH 229 A HOH 31 4 HOH HOH 230 A HOH 39 4 HOH HOH 231 A HOH 12 4 HOH HOH 232 A HOH 11 4 HOH HOH 233 A HOH 8 4 HOH HOH 234 A HOH 15 4 HOH HOH 235 A HOH 72 4 HOH HOH 236 A HOH 24 4 HOH HOH 237 A HOH 27 4 HOH HOH 238 A HOH 35 4 HOH HOH 239 A HOH 34 4 HOH HOH 240 A HOH 22 4 HOH HOH 241 A HOH 17 4 HOH HOH 242 A HOH 19 4 HOH HOH 243 A HOH 5 4 HOH HOH 244 A HOH 37 4 HOH HOH 245 A HOH 32 4 HOH HOH 246 A HOH 42 4 HOH HOH 247 A HOH 51 4 HOH HOH 248 A HOH 55 4 HOH HOH 249 A HOH 13 4 HOH HOH 250 A HOH 58 4 HOH HOH 251 A HOH 3 4 HOH HOH 252 A HOH 73 4 HOH HOH 253 A HOH 43 4 HOH HOH 254 A HOH 26 4 HOH HOH 255 A HOH 41 4 HOH HOH 256 A HOH 65 4 HOH HOH 257 A HOH 53 4 HOH HOH 258 A HOH 68 4 HOH HOH 259 A HOH 18 4 HOH HOH 260 A HOH 16 4 HOH HOH 261 A HOH 60 4 HOH HOH 262 A MET 1 n 1 MET 1 A GLN 2 n 2 GLN 2 A ILE 3 n 3 ILE 3 A PHE 4 n 4 PHE 4 A VAL 5 n 5 VAL 5 A LYS 6 n 6 LYS 6 A THR 7 n 7 THR 7 A LEU 8 n 8 LEU 8 A THR 9 n 9 THR 9 A GLY 10 n 10 GLY 10 A LYS 11 n 11 LYS 11 A TPO 12 n 12 TPO 12 A ILE 13 n 13 ILE 13 A THR 14 n 14 THR 14 A LEU 15 n 15 LEU 15 A GLU 16 n 16 GLU 16 A VAL 17 n 17 VAL 17 A GLU 18 n 18 GLU 18 A PRO 19 n 19 PRO 19 A SER 20 n 20 SER 20 A ASP 21 n 21 ASP 21 A THR 22 n 22 THR 22 A ILE 23 n 23 ILE 23 A GLU 24 n 24 GLU 24 A ASN 25 n 25 ASN 25 A VAL 26 n 26 VAL 26 A LYS 27 n 27 LYS 27 A ALA 28 n 28 ALA 28 A LYS 29 n 29 LYS 29 A ILE 30 n 30 ILE 30 A GLN 31 n 31 GLN 31 A ASP 32 n 32 ASP 32 A LYS 33 n 33 LYS 33 A GLU 34 n 34 GLU 34 A GLY 35 n 35 GLY 35 A ILE 36 n 36 ILE 36 A PRO 37 n 37 PRO 37 A PRO 38 n 38 PRO 38 A ASP 39 n 39 ASP 39 A GLN 40 n 40 GLN 40 A GLN 41 n 41 GLN 41 A ARG 42 n 42 ARG 42 A LEU 43 n 43 LEU 43 A ILE 44 n 44 ILE 44 A PHE 45 n 45 PHE 45 A ALA 46 n 46 ALA 46 A GLY 47 n 47 GLY 47 A LYS 48 n 48 LYS 48 A GLN 49 n 49 GLN 49 A LEU 50 n 50 LEU 50 A GLU 51 n 51 GLU 51 A ASP 52 n 52 ASP 52 A GLY 53 n 53 GLY 53 A ARG 54 n 54 ARG 54 A THR 55 n 55 THR 55 A LEU 56 n 56 LEU 56 A SER 57 n 57 SER 57 A ASP 58 n 58 ASP 58 A TYR 59 n 59 TYR 59 A ASN 60 n 60 ASN 60 A ILE 61 n 61 ILE 61 A GLN 62 n 62 GLN 62 A LYS 63 n 63 LYS 63 A GLU 64 n 64 GLU 64 A SER 65 n 65 SER 65 A THR 66 n 66 THR 66 A LEU 67 n 67 LEU 67 A HIS 68 n 68 HIS 68 A LEU 69 n 69 LEU 69 A VAL 70 n 70 VAL 70 A LEU 71 n 71 LEU 71 A ARG 72 n 72 ARG 72 A LEU 73 n 73 LEU 73 A ARG 74 n 74 ARG 74 A GLY 75 n 75 GLY 75 A GLY 76 n 76 GLY 76 A author_and_software_defined_assembly PISA 1 monomeric none 290 -4 4730 A TPO 12 modified residue A TPO 12 THR 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 O ILE 13 A O ILE 13 A N VAL 5 A N VAL 5 A N PHE 4 A N PHE 4 A O LEU 67 A O LEU 67 A O VAL 70 A O VAL 70 A N ARG 42 A N ARG 42 A N PHE 45 A N PHE 45 A O LYS 48 A O LYS 48 1 A CD LYS 63 A CD LYS 63 1 Y 1 A CE LYS 63 A CE LYS 63 1 Y 1 A NZ LYS 63 A NZ LYS 63 1 Y 1 A NH1 ARG 72 A NH1 ARG 72 1 Y 1 A A O O HOH HOH 230 256 1.62 1 A A O O HOH HOH 208 218 1.83 1 A A O O HOH HOH 208 254 1.91 1 A A O O HOH HOH 238 256 2.08 1 15.94 2.30 111.70 127.64 A A A CD CE NZ LYS LYS LYS 6 6 6 A A A N 1 -5.73 0.90 118.30 112.57 A A A CB CG OD2 ASP ASP ASP 32 32 32 N 1 6.18 0.50 120.30 126.48 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 1 3.03 0.50 120.30 123.33 A A A NE CZ NH1 ARG ARG ARG 54 54 54 A A A N 1 -3.35 0.50 120.30 116.95 A A A NE CZ NH2 ARG ARG ARG 54 54 54 A A A N 1 4.40 0.50 120.30 124.70 A A A NE CZ NH2 ARG ARG ARG 72 72 72 N 1 10.55 1.70 111.00 121.55 A A A CB CG CD1 LEU LEU LEU 73 73 73 N 1 A A CD OE2 GLU GLU 16 16 0.155 0.011 1.252 1.407 N 1 A A CD CE LYS LYS 27 27 -0.167 0.025 1.508 1.341 N 1 A A C O PRO PRO 37 37 0.126 0.020 1.228 1.354 N 1 A A CB CG ASP ASP 39 39 -0.180 0.021 1.513 1.333 N 1 A A CB OG SER SER 57 57 -0.099 0.013 1.418 1.319 B B N 1 A A O O HOH HOH 213 213 0.89 1_555 2_556 1 A A O O HOH HOH 209 225 1.03 1_555 3_455 1 A A O2P OD2 TPO ASP 12 52 1.73 B 1_555 1_545 1 A A O3 O PO4 HOH 101 217 1.80 1_555 3_545 1 A A O O HOH HOH 257 257 1.99 1_555 2_555 1 A A NZ O LYS HOH 6 221 2.10 B 1_555 1_545 1 A A O O GLY HOH 75 216 2.19 1_555 4_456 1 A A O O HOH HOH 203 256 2.19 1_555 1_545 1 A THR 9 -140.57 16.83 16.872 1.10 -0.00 -0.36 -0.84 -0.00 0.04 0.981 0.973 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.16653 0.12905 0.13092 1.07 43.81 1103 21851 4.8 95.13 1.234 0.027 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.034 0.036 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 1.07 43.81 62 676 12 0 602 0.037 0.019 780 0.003 0.020 766 3.261 2.035 1074 1.800 3.000 1804 7.429 5.000 108 30.112 25.758 33 15.250 15.000 158 14.835 15.000 5 0.190 0.200 125 0.013 0.021 882 0.010 0.020 132 3.504 1.252 381 3.314 1.248 380 4.889 1.885 492 4.887 1.896 493 4.442 1.629 399 4.437 1.628 399 4.990 2.297 577 19.515 17.945 823 19.486 17.500 811 7.268 3.000 1545 38.529 5.000 22 40.109 5.000 1568 0.303 0.262 1.098 84 1555 20 94.03 1.07 43.81 5NVG 22954 0.087 1 7.5 2.9 95.6 1.07 1.09 1 refinement REFMAC 5.8.0158 model building Coot phasing PHASER data reduction iMOSFLM data scaling Aimless N Polyubiquitin-B Thr12 Phosphorylated Ubiquitin 1 N N 2 N N 3 N N 4 N N A THR 22 A THR 22 HELX_P A GLY 35 A GLY 35 1 AA1 14 A PRO 37 A PRO 37 HELX_P A ASP 39 A ASP 39 5 AA2 3 A LEU 56 A LEU 56 HELX_P A ASN 60 A ASN 60 5 AA3 5 covale 1.301 both A A LYS 11 A C LYS 11 1_555 A TPO 12 A N TPO 12 1_555 covale 1.311 both B A LYS 11 A C LYS 11 1_555 A TPO 12 A N TPO 12 1_555 covale 1.347 both A A A TPO 12 A C TPO 12 1_555 A ILE 13 A N ILE 13 1_555 covale 1.340 both B B A TPO 12 A C TPO 12 1_555 A ILE 13 A N ILE 13 1_555 SIGNALING PROTEIN ubiquitin phosphoubiquitin phosphorylation phosphothreonine, signaling protein UBB_HUMAN UNP 1 1 P0CG47 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 1 76 5NVG 1 76 P0CG47 A 1 1 76 5 anti-parallel parallel anti-parallel anti-parallel A TPO 12 A TPO 12 A GLU 16 A GLU 16 A GLN 2 A GLN 2 A THR 7 A THR 7 A THR 66 A THR 66 A LEU 71 A LEU 71 A GLN 41 A GLN 41 A PHE 45 A PHE 45 A LYS 48 A LYS 48 A GLN 49 A GLN 49 binding site for residue PO4 A 101 A PO4 101 Software 8 binding site for residue PEG A 102 A PEG 102 Software 8 A LYS 11 A LYS 11 8 3_555 A ASP 39 A ASP 39 8 3_545 A PHE 45 A PHE 45 8 1_555 A LYS 48 A LYS 48 8 1_555 A TYR 59 A TYR 59 8 1_555 A ASN 60 A ASN 60 8 1_555 A HOH 207 D HOH 8 1_555 A HOH 217 D HOH 8 3_545 A PRO 19 A PRO 19 8 1_555 A SER 20 A SER 20 8 1_555 A SER 20 A SER 20 8 2_555 A THR 55 A THR 55 8 1_555 A THR 55 A THR 55 8 2_555 A SER 57 A SER 57 8 1_555 A ASP 58 A ASP 58 8 2_555 A HOH 210 D HOH 8 2_555 5 C 1 2 1