HEADER LIGASE 28-JAN-14 4ONN TITLE CRYSTAL STRUCTURE OF HUMAN MMS2/UBC13 - BAY 11-7082 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DDVIT 1, ENTEROCYTE DIFFERENTIATION-ASSOCIATED FACTOR 1, COMPND 5 EDAF-1, ENTEROCYTE DIFFERENTIATION-PROMOTING FACTOR 1, EDPF-1, MMS2 COMPND 6 HOMOLOG, VITAMIN D3-INDUCIBLE PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 N; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME, UBC13, UBCH13, COMPND 12 UBIQUITIN CARRIER PROTEIN N, UBIQUITIN-PROTEIN LIGASE N; COMPND 13 EC: 6.3.2.19; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMS2, UBE2V2, UEV2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: BLU, UBE2N; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX6P1 KEYWDS E2 UBIQUITIN CONJUGATING ENZYME, E1, E3, UBIQUITIN, COVALENT ADDUCT, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR C.D.HODGE,R.A.EDWARDS,J.N.M.GLOVER REVDAT 3 22-NOV-17 4ONN 1 REMARK REVDAT 2 05-AUG-15 4ONN 1 JRNL REVDAT 1 06-MAY-15 4ONN 0 JRNL AUTH C.D.HODGE,R.A.EDWARDS,C.J.MARKIN,D.MCDONALD,M.PULVINO, JRNL AUTH 2 M.S.HUEN,J.ZHAO,L.SPYRACOPOULOS,M.J.HENDZEL,J.N.GLOVER JRNL TITL COVALENT INHIBITION OF UBC13 AFFECTS UBIQUITIN SIGNALING AND JRNL TITL 2 REVEALS ACTIVE SITE ELEMENTS IMPORTANT FOR TARGETING. JRNL REF ACS CHEM.BIOL. V. 10 1718 2015 JRNL REFN ISSN 1554-8929 JRNL PMID 25909880 JRNL DOI 10.1021/ACSCHEMBIO.5B00222 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3_1479 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 47161 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.310 REMARK 3 FREE R VALUE TEST SET COUNT : 2635 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.7660 - 4.6563 1.00 2998 156 0.1602 0.1596 REMARK 3 2 4.6563 - 3.6964 1.00 3018 147 0.1491 0.1750 REMARK 3 3 3.6964 - 3.2293 1.00 3000 146 0.1640 0.1690 REMARK 3 4 3.2293 - 2.9341 1.00 3007 183 0.1779 0.2514 REMARK 3 5 2.9341 - 2.7238 1.00 3019 148 0.1818 0.2351 REMARK 3 6 2.7238 - 2.5632 1.00 2960 183 0.1823 0.2310 REMARK 3 7 2.5632 - 2.4349 1.00 3005 177 0.1705 0.2316 REMARK 3 8 2.4349 - 2.3289 1.00 2965 165 0.1775 0.2253 REMARK 3 9 2.3289 - 2.2392 1.00 2978 178 0.1730 0.1996 REMARK 3 10 2.2392 - 2.1619 1.00 2974 209 0.1772 0.2017 REMARK 3 11 2.1619 - 2.0943 1.00 3043 149 0.1752 0.2237 REMARK 3 12 2.0943 - 2.0345 1.00 2958 137 0.1711 0.2114 REMARK 3 13 2.0345 - 1.9809 1.00 3010 181 0.1781 0.2326 REMARK 3 14 1.9809 - 1.9326 1.00 2977 167 0.1836 0.2080 REMARK 3 15 1.9326 - 1.8887 1.00 3036 138 0.1798 0.2434 REMARK 3 16 1.8887 - 1.8485 1.00 2988 156 0.1788 0.2447 REMARK 3 17 1.8485 - 1.8115 1.00 3012 170 0.1907 0.2418 REMARK 3 18 1.8115 - 1.7773 1.00 2929 194 0.1955 0.2094 REMARK 3 19 1.7773 - 1.7456 1.00 3006 191 0.1990 0.2629 REMARK 3 20 1.7456 - 1.7160 1.00 2992 157 0.2175 0.2475 REMARK 3 21 1.7160 - 1.6883 1.00 2974 189 0.2088 0.2137 REMARK 3 22 1.6883 - 1.6623 1.00 2977 173 0.2174 0.2659 REMARK 3 23 1.6623 - 1.6379 1.00 2996 156 0.2281 0.2361 REMARK 3 24 1.6379 - 1.6148 1.00 3016 167 0.2367 0.2583 REMARK 3 25 1.6148 - 1.5930 1.00 2969 155 0.2409 0.2748 REMARK 3 26 1.5930 - 1.5723 1.00 3037 160 0.2533 0.2825 REMARK 3 27 1.5723 - 1.5526 1.00 2955 171 0.2534 0.2933 REMARK 3 28 1.5526 - 1.5339 1.00 3023 156 0.2625 0.2777 REMARK 3 29 1.5339 - 1.5161 1.00 2977 219 0.2828 0.2815 REMARK 3 30 1.5161 - 1.5000 0.97 2866 151 0.3030 0.3335 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2438 REMARK 3 ANGLE : 1.144 3314 REMARK 3 CHIRALITY : 0.077 354 REMARK 3 PLANARITY : 0.005 437 REMARK 3 DIHEDRAL : 13.506 948 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 16 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0957 14.2108 18.7585 REMARK 3 T TENSOR REMARK 3 T11: 0.1692 T22: 0.1731 REMARK 3 T33: 0.1787 T12: -0.0167 REMARK 3 T13: -0.0177 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 1.9636 L22: 1.8835 REMARK 3 L33: 9.2692 L12: -0.7410 REMARK 3 L13: 0.2614 L23: 1.5149 REMARK 3 S TENSOR REMARK 3 S11: -0.1077 S12: -0.0240 S13: -0.1689 REMARK 3 S21: 0.3219 S22: -0.0821 S23: -0.0748 REMARK 3 S31: 0.6161 S32: 0.1375 S33: 0.1753 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 36 THROUGH 61 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6325 19.5016 7.2721 REMARK 3 T TENSOR REMARK 3 T11: 0.0922 T22: 0.1251 REMARK 3 T33: 0.1187 T12: -0.0245 REMARK 3 T13: 0.0185 T23: 0.0274 REMARK 3 L TENSOR REMARK 3 L11: 4.5660 L22: 1.6026 REMARK 3 L33: 5.6938 L12: 0.3180 REMARK 3 L13: 3.0055 L23: 0.6789 REMARK 3 S TENSOR REMARK 3 S11: -0.2119 S12: 0.3406 S13: 0.0900 REMARK 3 S21: -0.0890 S22: 0.1304 S23: -0.1428 REMARK 3 S31: -0.3167 S32: 0.5367 S33: 0.0363 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 62 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6131 21.6241 12.5574 REMARK 3 T TENSOR REMARK 3 T11: 0.1030 T22: 0.0895 REMARK 3 T33: 0.1248 T12: 0.0136 REMARK 3 T13: -0.0032 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 1.7156 L22: 1.8541 REMARK 3 L33: 8.5319 L12: 0.1627 REMARK 3 L13: 1.3917 L23: -0.2210 REMARK 3 S TENSOR REMARK 3 S11: -0.1455 S12: -0.0374 S13: 0.1605 REMARK 3 S21: 0.1954 S22: 0.0446 S23: 0.0396 REMARK 3 S31: -0.4030 S32: 0.1213 S33: 0.1115 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5337 20.0811 9.5817 REMARK 3 T TENSOR REMARK 3 T11: 0.1276 T22: 0.2055 REMARK 3 T33: 0.2064 T12: 0.0343 REMARK 3 T13: 0.0138 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 1.2951 L22: 5.4004 REMARK 3 L33: 6.9527 L12: 0.4640 REMARK 3 L13: 1.4430 L23: -3.5984 REMARK 3 S TENSOR REMARK 3 S11: -0.1578 S12: 0.0032 S13: 0.2266 REMARK 3 S21: 0.2670 S22: 0.1906 S23: 0.4614 REMARK 3 S31: -0.3879 S32: -0.5020 S33: -0.0853 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 108 THROUGH 127 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.1034 10.6987 13.7377 REMARK 3 T TENSOR REMARK 3 T11: 0.1300 T22: 0.0926 REMARK 3 T33: 0.1662 T12: 0.0013 REMARK 3 T13: 0.0120 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 2.4475 L22: 2.5521 REMARK 3 L33: 5.5871 L12: 0.2004 REMARK 3 L13: 1.6149 L23: -0.2011 REMARK 3 S TENSOR REMARK 3 S11: 0.0848 S12: 0.0372 S13: -0.2157 REMARK 3 S21: 0.2322 S22: 0.0218 S23: 0.1129 REMARK 3 S31: 0.1895 S32: 0.0410 S33: -0.1100 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 128 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8539 19.5265 -1.9516 REMARK 3 T TENSOR REMARK 3 T11: 0.1234 T22: 0.1907 REMARK 3 T33: 0.1396 T12: 0.0248 REMARK 3 T13: -0.0260 T23: -0.0283 REMARK 3 L TENSOR REMARK 3 L11: 8.4443 L22: 1.4364 REMARK 3 L33: 6.4688 L12: 2.6279 REMARK 3 L13: -0.5409 L23: -1.6938 REMARK 3 S TENSOR REMARK 3 S11: -0.1638 S12: 0.1891 S13: 0.2494 REMARK 3 S21: -0.1648 S22: 0.1021 S23: 0.1208 REMARK 3 S31: -0.2216 S32: 0.1488 S33: 0.0135 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4435 11.2278 47.6725 REMARK 3 T TENSOR REMARK 3 T11: 0.3953 T22: 0.3969 REMARK 3 T33: 0.4063 T12: -0.0346 REMARK 3 T13: 0.0282 T23: 0.1389 REMARK 3 L TENSOR REMARK 3 L11: 8.5591 L22: 6.8213 REMARK 3 L33: 6.6840 L12: 0.4151 REMARK 3 L13: -1.4984 L23: 1.4921 REMARK 3 S TENSOR REMARK 3 S11: 0.2388 S12: -0.5236 S13: 0.2292 REMARK 3 S21: 0.0293 S22: -0.3237 S23: -0.7467 REMARK 3 S31: -0.3631 S32: 0.8081 S33: 0.0692 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.8374 21.9671 44.0742 REMARK 3 T TENSOR REMARK 3 T11: 0.4696 T22: 0.3553 REMARK 3 T33: 0.2787 T12: -0.1120 REMARK 3 T13: 0.0028 T23: 0.0795 REMARK 3 L TENSOR REMARK 3 L11: 4.1529 L22: 2.7120 REMARK 3 L33: 0.9897 L12: 3.3262 REMARK 3 L13: 1.3318 L23: 1.1990 REMARK 3 S TENSOR REMARK 3 S11: 0.3223 S12: -0.6508 S13: 0.0176 REMARK 3 S21: 0.7879 S22: -0.3053 S23: 0.1642 REMARK 3 S31: -0.0580 S32: -0.2733 S33: -0.0376 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 34 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.1268 28.5369 36.9899 REMARK 3 T TENSOR REMARK 3 T11: 0.2173 T22: 0.1476 REMARK 3 T33: 0.1388 T12: 0.0065 REMARK 3 T13: -0.0539 T23: 0.0355 REMARK 3 L TENSOR REMARK 3 L11: 5.2496 L22: 7.1064 REMARK 3 L33: 1.7811 L12: 4.4474 REMARK 3 L13: -0.3351 L23: 0.6015 REMARK 3 S TENSOR REMARK 3 S11: 0.2808 S12: -0.1375 S13: 0.0081 REMARK 3 S21: 0.5566 S22: -0.0798 S23: -0.0674 REMARK 3 S31: 0.1076 S32: -0.0082 S33: -0.2078 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 58 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.6536 17.3429 32.5240 REMARK 3 T TENSOR REMARK 3 T11: 0.2516 T22: 0.1563 REMARK 3 T33: 0.2341 T12: -0.0095 REMARK 3 T13: 0.0112 T23: 0.0224 REMARK 3 L TENSOR REMARK 3 L11: 2.9909 L22: 7.2928 REMARK 3 L33: 3.2339 L12: 1.6424 REMARK 3 L13: -1.6222 L23: -3.1050 REMARK 3 S TENSOR REMARK 3 S11: -0.3587 S12: -0.0745 S13: -0.5082 REMARK 3 S21: -0.4030 S22: 0.2823 S23: 0.1746 REMARK 3 S31: 0.6211 S32: -0.2034 S33: 0.0473 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 77 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.5862 24.6987 24.9342 REMARK 3 T TENSOR REMARK 3 T11: 0.1577 T22: 0.1579 REMARK 3 T33: 0.1943 T12: 0.0249 REMARK 3 T13: -0.0178 T23: -0.0388 REMARK 3 L TENSOR REMARK 3 L11: 2.0145 L22: 5.2384 REMARK 3 L33: 4.3452 L12: 0.9497 REMARK 3 L13: 1.2859 L23: -0.2310 REMARK 3 S TENSOR REMARK 3 S11: 0.0629 S12: 0.4192 S13: -0.2442 REMARK 3 S21: -0.0998 S22: 0.0951 S23: -0.3674 REMARK 3 S31: 0.3633 S32: 0.0160 S33: -0.1131 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 87 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.2233 11.5359 34.4827 REMARK 3 T TENSOR REMARK 3 T11: 0.4912 T22: 0.5358 REMARK 3 T33: 0.6578 T12: 0.0797 REMARK 3 T13: 0.0941 T23: 0.2614 REMARK 3 L TENSOR REMARK 3 L11: 2.1712 L22: 5.1041 REMARK 3 L33: 9.0015 L12: 2.6155 REMARK 3 L13: -3.0618 L23: -6.7374 REMARK 3 S TENSOR REMARK 3 S11: -0.2729 S12: -0.5288 S13: -1.0202 REMARK 3 S21: -0.3107 S22: -0.3546 S23: -0.8405 REMARK 3 S31: 0.9861 S32: 0.9180 S33: 0.6747 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.9148 21.5968 39.7582 REMARK 3 T TENSOR REMARK 3 T11: 0.2354 T22: 0.3379 REMARK 3 T33: 0.2923 T12: 0.0299 REMARK 3 T13: -0.0375 T23: 0.1228 REMARK 3 L TENSOR REMARK 3 L11: 5.0573 L22: 7.0810 REMARK 3 L33: 8.1115 L12: 4.7637 REMARK 3 L13: -5.1519 L23: -6.4315 REMARK 3 S TENSOR REMARK 3 S11: -0.0535 S12: -1.2174 S13: -0.9418 REMARK 3 S21: 0.4853 S22: -0.3866 S23: -0.6089 REMARK 3 S31: -0.0855 S32: 0.2751 S33: 0.3946 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 114 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.1736 22.9393 24.5733 REMARK 3 T TENSOR REMARK 3 T11: 0.2591 T22: 0.3116 REMARK 3 T33: 0.4314 T12: 0.0294 REMARK 3 T13: 0.0189 T23: -0.0760 REMARK 3 L TENSOR REMARK 3 L11: 1.5324 L22: 3.5431 REMARK 3 L33: 7.0944 L12: 0.8664 REMARK 3 L13: 0.3984 L23: 4.8316 REMARK 3 S TENSOR REMARK 3 S11: 0.0336 S12: 0.2195 S13: -0.3937 REMARK 3 S21: 0.0106 S22: -0.0239 S23: -0.3672 REMARK 3 S31: 0.3185 S32: -0.2773 S33: 0.0300 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 124 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.7226 31.3172 21.0783 REMARK 3 T TENSOR REMARK 3 T11: 0.3949 T22: 0.3552 REMARK 3 T33: 0.5772 T12: 0.1065 REMARK 3 T13: 0.1868 T23: -0.0152 REMARK 3 L TENSOR REMARK 3 L11: 3.4812 L22: 7.3166 REMARK 3 L33: 7.1670 L12: 3.9177 REMARK 3 L13: 3.9377 L23: 1.6314 REMARK 3 S TENSOR REMARK 3 S11: 0.5921 S12: 1.3176 S13: 0.1698 REMARK 3 S21: -1.3922 S22: -0.1681 S23: -0.6900 REMARK 3 S31: -0.4042 S32: 0.5119 S33: -0.3896 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 133 THROUGH 150 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.9814 38.8858 28.3274 REMARK 3 T TENSOR REMARK 3 T11: 0.1848 T22: 0.1147 REMARK 3 T33: 0.1633 T12: 0.0123 REMARK 3 T13: -0.0052 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 2.0011 L22: 8.2280 REMARK 3 L33: 6.7003 L12: -1.1681 REMARK 3 L13: -0.8540 L23: 0.2429 REMARK 3 S TENSOR REMARK 3 S11: 0.1397 S12: -0.3470 S13: 0.1103 REMARK 3 S21: -0.0104 S22: 0.0919 S23: -0.3788 REMARK 3 S31: -0.2027 S32: 0.1147 S33: -0.2231 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ONN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084720. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97947 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47161 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE, 15% PEG 8000, REMARK 280 PH 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 22.36500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.76550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.26650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.76550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.36500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.26650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -7 REMARK 465 PRO A -6 REMARK 465 LEU A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 PRO A -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 REMARK 465 SER A 4 REMARK 465 THR A 5 REMARK 465 GLY B -7 REMARK 465 PRO B -6 REMARK 465 LEU B -5 REMARK 465 GLY B -4 REMARK 465 SER B -3 REMARK 465 PRO B -2 REMARK 465 GLU B -1 REMARK 465 PHE B 0 REMARK 465 MET B 1 REMARK 465 ASN B 151 REMARK 465 ILE B 152 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS B 92 -95.43 -144.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE COMPOUND BY1 LOSES THE 4-METHYLBENZENE-SULFINIC ACID GROUP ON REMARK 600 INERACTING WITH UBC13 AND THE REMAINING PART OF BY1 FORMS A REMARK 600 COVALENT BOND WITH THE SG ATOM OF CYS B87 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BY1 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ONL RELATED DB: PDB REMARK 900 RELATED ID: 4ONM RELATED DB: PDB DBREF 4ONN A 1 145 UNP Q15819 UB2V2_HUMAN 1 145 DBREF 4ONN B 1 152 UNP P61088 UBE2N_HUMAN 1 152 SEQADV 4ONN GLY A -7 UNP Q15819 EXPRESSION TAG SEQADV 4ONN PRO A -6 UNP Q15819 EXPRESSION TAG SEQADV 4ONN LEU A -5 UNP Q15819 EXPRESSION TAG SEQADV 4ONN GLY A -4 UNP Q15819 EXPRESSION TAG SEQADV 4ONN SER A -3 UNP Q15819 EXPRESSION TAG SEQADV 4ONN PRO A -2 UNP Q15819 EXPRESSION TAG SEQADV 4ONN GLU A -1 UNP Q15819 EXPRESSION TAG SEQADV 4ONN PHE A 0 UNP Q15819 EXPRESSION TAG SEQADV 4ONN GLY B -7 UNP P61088 EXPRESSION TAG SEQADV 4ONN PRO B -6 UNP P61088 EXPRESSION TAG SEQADV 4ONN LEU B -5 UNP P61088 EXPRESSION TAG SEQADV 4ONN GLY B -4 UNP P61088 EXPRESSION TAG SEQADV 4ONN SER B -3 UNP P61088 EXPRESSION TAG SEQADV 4ONN PRO B -2 UNP P61088 EXPRESSION TAG SEQADV 4ONN GLU B -1 UNP P61088 EXPRESSION TAG SEQADV 4ONN PHE B 0 UNP P61088 EXPRESSION TAG SEQRES 1 A 153 GLY PRO LEU GLY SER PRO GLU PHE MET ALA VAL SER THR SEQRES 2 A 153 GLY VAL LYS VAL PRO ARG ASN PHE ARG LEU LEU GLU GLU SEQRES 3 A 153 LEU GLU GLU GLY GLN LYS GLY VAL GLY ASP GLY THR VAL SEQRES 4 A 153 SER TRP GLY LEU GLU ASP ASP GLU ASP MET THR LEU THR SEQRES 5 A 153 ARG TRP THR GLY MET ILE ILE GLY PRO PRO ARG THR ASN SEQRES 6 A 153 TYR GLU ASN ARG ILE TYR SER LEU LYS VAL GLU CYS GLY SEQRES 7 A 153 PRO LYS TYR PRO GLU ALA PRO PRO SER VAL ARG PHE VAL SEQRES 8 A 153 THR LYS ILE ASN MET ASN GLY ILE ASN ASN SER SER GLY SEQRES 9 A 153 MET VAL ASP ALA ARG SER ILE PRO VAL LEU ALA LYS TRP SEQRES 10 A 153 GLN ASN SER TYR SER ILE LYS VAL VAL LEU GLN GLU LEU SEQRES 11 A 153 ARG ARG LEU MET MET SER LYS GLU ASN MET LYS LEU PRO SEQRES 12 A 153 GLN PRO PRO GLU GLY GLN THR TYR ASN ASN SEQRES 1 B 160 GLY PRO LEU GLY SER PRO GLU PHE MET ALA GLY LEU PRO SEQRES 2 B 160 ARG ARG ILE ILE LYS GLU THR GLN ARG LEU LEU ALA GLU SEQRES 3 B 160 PRO VAL PRO GLY ILE LYS ALA GLU PRO ASP GLU SER ASN SEQRES 4 B 160 ALA ARG TYR PHE HIS VAL VAL ILE ALA GLY PRO GLN ASP SEQRES 5 B 160 SER PRO PHE GLU GLY GLY THR PHE LYS LEU GLU LEU PHE SEQRES 6 B 160 LEU PRO GLU GLU TYR PRO MET ALA ALA PRO LYS VAL ARG SEQRES 7 B 160 PHE MET THR LYS ILE TYR HIS PRO ASN VAL ASP LYS LEU SEQRES 8 B 160 GLY ARG ILE CYS LEU ASP ILE LEU LYS ASP LYS TRP SER SEQRES 9 B 160 PRO ALA LEU GLN ILE ARG THR VAL LEU LEU SER ILE GLN SEQRES 10 B 160 ALA LEU LEU SER ALA PRO ASN PRO ASP ASP PRO LEU ALA SEQRES 11 B 160 ASN ASP VAL ALA GLU GLN TRP LYS THR ASN GLU ALA GLN SEQRES 12 B 160 ALA ILE GLU THR ALA ARG ALA TRP THR ARG LEU TYR ALA SEQRES 13 B 160 MET ASN ASN ILE HET GOL A 201 6 HET GOL A 202 6 HET BY1 B 201 4 HET GOL B 202 6 HETNAM GOL GLYCEROL HETNAM BY1 3-[(4-METHYLPHENYL)SULFONYL]PROP-2-ENENITRILE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN BY1 BAY 11-7082 FORMUL 3 GOL 3(C3 H8 O3) FORMUL 5 BY1 C10 H9 N O2 S FORMUL 7 HOH *183(H2 O) HELIX 1 1 PRO A 10 GLY A 25 1 16 HELIX 2 2 ASP A 99 SER A 102 5 4 HELIX 3 3 ILE A 103 LYS A 108 1 6 HELIX 4 4 SER A 114 MET A 126 1 13 HELIX 5 5 PRO B 5 GLU B 18 1 14 HELIX 6 6 LEU B 88 LYS B 92 5 5 HELIX 7 7 GLN B 100 ALA B 114 1 15 HELIX 8 8 VAL B 125 ASN B 132 1 8 HELIX 9 9 ASN B 132 ALA B 148 1 17 SHEET 1 A 4 VAL A 31 LEU A 35 0 SHEET 2 A 4 ARG A 45 ILE A 51 -1 O THR A 47 N GLY A 34 SHEET 3 A 4 ILE A 62 GLU A 68 -1 O TYR A 63 N ILE A 50 SHEET 4 A 4 SER A 79 PHE A 82 -1 O SER A 79 N GLU A 68 SHEET 1 B 4 ILE B 23 PRO B 27 0 SHEET 2 B 4 TYR B 34 ALA B 40 -1 O HIS B 36 N GLU B 26 SHEET 3 B 4 THR B 51 PHE B 57 -1 O LEU B 56 N PHE B 35 SHEET 4 B 4 LYS B 68 PHE B 71 -1 O LYS B 68 N PHE B 57 LINK SG CYS B 87 C12 BY1 B 201 1555 1555 1.75 CISPEP 1 TYR A 73 PRO A 74 0 1.24 CISPEP 2 TYR B 62 PRO B 63 0 7.80 SITE 1 AC1 4 ASN A 60 GLY A 90 ILE A 91 ASN A 93 SITE 1 AC2 6 ASN A 89 SER A 102 ILE A 103 PRO A 104 SITE 2 AC2 6 GLU A 130 ASN A 131 SITE 1 AC3 10 PRO B 78 ASN B 79 VAL B 80 ASP B 81 SITE 2 AC3 10 CYS B 87 LEU B 121 ASN B 123 HOH B 301 SITE 3 AC3 10 HOH B 302 HOH B 319 SITE 1 AC4 5 LYS B 68 VAL B 69 ARG B 85 ILE B 86 SITE 2 AC4 5 HOH B 320 CRYST1 44.730 74.533 91.531 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022356 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010925 0.00000