HEADER LIGASE 23-SEP-25 9YE9 TITLE STRUCTURE OF UBCH5B IN COMPLEX WITH THE U-BOX DOMAIN OF THE E3 TITLE 2 UBIQUITIN LIGASE CHIP COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D2,E2 COMPND 5 UBIQUITIN-CONJUGATING ENZYME D2,UBIQUITIN CARRIER PROTEIN D2, COMPND 6 UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2,UBIQUITIN-CONJUGATING ENZYME COMPND 7 E2-17 KDA 2,UBIQUITIN-PROTEIN LIGASE D2,P53-REGULATED UBIQUITIN- COMPND 8 CONJUGATING ENZYME 1; COMPND 9 EC: 2.3.2.23,2.3.2.24; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE CHIP; COMPND 14 CHAIN: B, C; COMPND 15 SYNONYM: RING-TYPE E3 UBIQUITIN TRANSFERASE CHIP,STIP1 HOMOLOGY AND U COMPND 16 BOX-CONTAINING PROTEIN 1; COMPND 17 EC: 2.3.2.27; COMPND 18 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: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 10 ORGANISM_COMMON: ZEBRAFISH; SOURCE 11 ORGANISM_TAXID: 7955; SOURCE 12 GENE: STUB1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS UBIQUITIN CONJUGATING ENZYME, UBIQUITIN LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.M.MANAGE,J.C.NIX,R.C.PAGE REVDAT 2 12-NOV-25 9YE9 1 JRNL REVDAT 1 05-NOV-25 9YE9 0 JRNL AUTH M.M.MANAGE,J.C.NIX,R.C.PAGE JRNL TITL FUNCTIONAL AND STRUCTURAL ANALYSES OF UBCH5 MUTANTS WITH JRNL TITL 2 ENHANCED BINDING TO THE E3 UBIQUITIN LIGASE CHIP. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 789 52873 2025 JRNL REFN ESSN 1090-2104 JRNL PMID 41167006 JRNL DOI 10.1016/J.BBRC.2025.152873 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 46470 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.570 REMARK 3 FREE R VALUE TEST SET COUNT : 3520 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 41.4400 - 5.8700 1.00 1847 146 0.1665 0.2034 REMARK 3 2 5.8700 - 4.6600 0.99 1835 157 0.1733 0.2039 REMARK 3 3 4.6600 - 4.0700 1.00 1844 146 0.1648 0.2055 REMARK 3 4 4.0700 - 3.7000 0.94 1725 144 0.1996 0.2055 REMARK 3 5 3.7000 - 3.4400 0.93 1731 138 0.2499 0.3396 REMARK 3 6 3.4400 - 3.2300 0.99 1831 149 0.2206 0.2517 REMARK 3 7 3.2300 - 3.0700 0.99 1838 143 0.2346 0.2905 REMARK 3 8 3.0700 - 2.9400 0.99 1839 152 0.2373 0.3470 REMARK 3 9 2.9400 - 2.8300 0.99 1817 157 0.2628 0.3430 REMARK 3 10 2.8300 - 2.7300 1.00 1857 157 0.2625 0.3461 REMARK 3 11 2.7300 - 2.6400 1.00 1830 147 0.2690 0.3444 REMARK 3 12 2.6400 - 2.5700 1.00 1852 151 0.2624 0.3371 REMARK 3 13 2.5700 - 2.5000 1.00 1819 147 0.2687 0.3312 REMARK 3 14 2.5000 - 2.4400 0.99 1840 148 0.2940 0.3098 REMARK 3 15 2.4400 - 2.3800 0.99 1848 151 0.3035 0.3510 REMARK 3 16 2.3800 - 2.3300 1.00 1824 143 0.3102 0.4125 REMARK 3 17 2.3300 - 2.2900 0.86 1604 143 0.3847 0.4822 REMARK 3 18 2.2900 - 2.2500 0.38 637 51 0.5144 0.4195 REMARK 3 19 2.2400 - 2.2000 0.38 699 47 0.4880 0.5951 REMARK 3 20 2.2000 - 2.1700 0.93 1729 150 0.4190 0.4738 REMARK 3 21 2.1700 - 2.1300 0.99 1812 162 0.3459 0.3519 REMARK 3 22 2.1300 - 2.1000 0.99 1838 146 0.3590 0.4054 REMARK 3 23 2.1000 - 2.0700 0.99 1835 153 0.3709 0.3614 REMARK 3 24 2.0700 - 2.0400 0.98 1805 145 0.3792 0.3877 REMARK 3 25 2.0400 - 2.0100 0.97 1814 147 0.4062 0.4834 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.46 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 : 0.009 2405 REMARK 3 ANGLE : 1.045 3260 REMARK 3 CHIRALITY : 0.060 357 REMARK 3 PLANARITY : 0.011 427 REMARK 3 DIHEDRAL : 15.891 911 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 17 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -4 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.3364 -27.8836 10.7418 REMARK 3 T TENSOR REMARK 3 T11: 0.3811 T22: 0.5155 REMARK 3 T33: 0.3164 T12: -0.0904 REMARK 3 T13: -0.0954 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 8.7760 L22: 5.7569 REMARK 3 L33: 3.2128 L12: -3.1350 REMARK 3 L13: 1.2707 L23: -1.5330 REMARK 3 S TENSOR REMARK 3 S11: 0.6095 S12: 0.1930 S13: -0.4314 REMARK 3 S21: -0.3398 S22: -0.2034 S23: 0.2751 REMARK 3 S31: 0.4696 S32: -0.1013 S33: -0.4151 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0813 -33.2193 18.9801 REMARK 3 T TENSOR REMARK 3 T11: 0.5268 T22: 0.5002 REMARK 3 T33: 0.4035 T12: 0.0606 REMARK 3 T13: -0.1395 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 6.7439 L22: 7.8527 REMARK 3 L33: 7.7149 L12: 0.2598 REMARK 3 L13: 5.9916 L23: -0.3728 REMARK 3 S TENSOR REMARK 3 S11: 0.3963 S12: 1.9045 S13: 0.3479 REMARK 3 S21: -0.5229 S22: -0.0891 S23: -0.4981 REMARK 3 S31: 0.3191 S32: 1.4802 S33: -0.2863 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1551 -27.2974 25.6866 REMARK 3 T TENSOR REMARK 3 T11: 0.4037 T22: 0.2832 REMARK 3 T33: 0.2357 T12: 0.0173 REMARK 3 T13: -0.0355 T23: 0.0393 REMARK 3 L TENSOR REMARK 3 L11: 5.8466 L22: 3.0649 REMARK 3 L33: 6.0719 L12: 0.2852 REMARK 3 L13: 5.3522 L23: -0.0209 REMARK 3 S TENSOR REMARK 3 S11: 0.2637 S12: -0.3461 S13: -0.5396 REMARK 3 S21: 0.2167 S22: 0.2614 S23: -0.1994 REMARK 3 S31: 0.3349 S32: -0.5226 S33: -0.4887 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 56 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.9960 -17.2544 24.0959 REMARK 3 T TENSOR REMARK 3 T11: 0.2558 T22: 0.1494 REMARK 3 T33: 0.2178 T12: 0.0287 REMARK 3 T13: 0.0029 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 3.5384 L22: 1.5530 REMARK 3 L33: 7.3473 L12: 0.0733 REMARK 3 L13: 2.4554 L23: 0.1845 REMARK 3 S TENSOR REMARK 3 S11: -0.1007 S12: -0.2411 S13: 0.0652 REMARK 3 S21: 0.3779 S22: 0.2462 S23: -0.1019 REMARK 3 S31: -0.3900 S32: -0.0908 S33: -0.1306 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 85 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1813 -14.2123 13.9854 REMARK 3 T TENSOR REMARK 3 T11: 0.3747 T22: 0.2839 REMARK 3 T33: 0.2577 T12: -0.0573 REMARK 3 T13: -0.0591 T23: 0.0418 REMARK 3 L TENSOR REMARK 3 L11: 7.4822 L22: 3.6902 REMARK 3 L33: 5.5340 L12: 2.7950 REMARK 3 L13: 5.2538 L23: 3.9724 REMARK 3 S TENSOR REMARK 3 S11: -0.5931 S12: 0.3857 S13: 0.5297 REMARK 3 S21: -0.3263 S22: 0.4789 S23: -0.3092 REMARK 3 S31: -1.2455 S32: 0.8209 S33: 0.1215 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.3580 -22.4874 18.4790 REMARK 3 T TENSOR REMARK 3 T11: 0.3445 T22: 0.2458 REMARK 3 T33: 0.3176 T12: 0.1155 REMARK 3 T13: -0.0086 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 7.0357 L22: 5.7364 REMARK 3 L33: 9.4004 L12: 3.2080 REMARK 3 L13: 6.8949 L23: 3.3122 REMARK 3 S TENSOR REMARK 3 S11: 0.3473 S12: 0.6454 S13: -0.8499 REMARK 3 S21: 0.5250 S22: 0.2304 S23: -0.4742 REMARK 3 S31: 1.1768 S32: 1.1937 S33: -0.5156 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 112 THROUGH 130 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1168 -9.9390 28.7248 REMARK 3 T TENSOR REMARK 3 T11: 0.3256 T22: 0.3348 REMARK 3 T33: 0.2988 T12: -0.0273 REMARK 3 T13: -0.1234 T23: -0.0204 REMARK 3 L TENSOR REMARK 3 L11: 8.6201 L22: 4.8892 REMARK 3 L33: 2.8522 L12: 0.4650 REMARK 3 L13: 0.5697 L23: 0.7712 REMARK 3 S TENSOR REMARK 3 S11: -0.4500 S12: 0.9383 S13: 0.4201 REMARK 3 S21: -0.4409 S22: 0.2846 S23: -0.0078 REMARK 3 S31: -0.4187 S32: 0.1979 S33: 0.1243 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 131 THROUGH 147 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1618 -21.7755 36.5224 REMARK 3 T TENSOR REMARK 3 T11: 0.5747 T22: 0.2798 REMARK 3 T33: 0.4036 T12: 0.0596 REMARK 3 T13: -0.2019 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 9.0156 L22: 6.0733 REMARK 3 L33: 0.7312 L12: 3.1692 REMARK 3 L13: -0.2141 L23: -0.6128 REMARK 3 S TENSOR REMARK 3 S11: 0.6211 S12: -0.6153 S13: -0.4029 REMARK 3 S21: 1.2879 S22: -0.4335 S23: -0.7652 REMARK 3 S31: 0.0206 S32: 0.1581 S33: -0.1371 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 207 THROUGH 212 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4234 -32.5817 -3.2848 REMARK 3 T TENSOR REMARK 3 T11: 0.8799 T22: 0.6973 REMARK 3 T33: 1.1049 T12: 0.0056 REMARK 3 T13: -0.0586 T23: 0.1889 REMARK 3 L TENSOR REMARK 3 L11: 3.1822 L22: 3.3321 REMARK 3 L33: 4.4751 L12: -2.1664 REMARK 3 L13: 2.9693 L23: -3.8008 REMARK 3 S TENSOR REMARK 3 S11: -0.1514 S12: -1.7034 S13: -2.7026 REMARK 3 S21: -1.0181 S22: 0.1867 S23: -2.4040 REMARK 3 S31: 2.9686 S32: -0.3448 S33: -0.0865 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 213 THROUGH 223 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.4594 -24.5374 -1.5582 REMARK 3 T TENSOR REMARK 3 T11: 0.4729 T22: 0.5326 REMARK 3 T33: 0.4391 T12: -0.1372 REMARK 3 T13: 0.0729 T23: -0.1244 REMARK 3 L TENSOR REMARK 3 L11: 6.7069 L22: 7.5137 REMARK 3 L33: 7.3238 L12: 1.0207 REMARK 3 L13: 3.9663 L23: 1.8534 REMARK 3 S TENSOR REMARK 3 S11: 0.1394 S12: 0.7720 S13: -1.2215 REMARK 3 S21: 0.1920 S22: -0.1201 S23: 0.2329 REMARK 3 S31: 1.5084 S32: -0.5269 S33: -0.0376 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 224 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.6040 -15.9945 -7.0680 REMARK 3 T TENSOR REMARK 3 T11: 0.3729 T22: 0.6633 REMARK 3 T33: 0.2615 T12: -0.1104 REMARK 3 T13: 0.0140 T23: 0.0649 REMARK 3 L TENSOR REMARK 3 L11: 2.1973 L22: 3.4609 REMARK 3 L33: 5.4381 L12: -0.1867 REMARK 3 L13: 2.5851 L23: 2.5593 REMARK 3 S TENSOR REMARK 3 S11: 0.0289 S12: 0.2172 S13: -0.1600 REMARK 3 S21: 0.3955 S22: -0.0289 S23: 0.2194 REMARK 3 S31: 0.0279 S32: -0.1407 S33: 0.0496 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 232 THROUGH 244 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3816 -14.3320 -0.3218 REMARK 3 T TENSOR REMARK 3 T11: 0.2475 T22: 0.5451 REMARK 3 T33: 0.2491 T12: 0.0376 REMARK 3 T13: 0.0207 T23: 0.0892 REMARK 3 L TENSOR REMARK 3 L11: 3.9079 L22: 8.2979 REMARK 3 L33: 6.6887 L12: 2.0092 REMARK 3 L13: -3.6444 L23: 2.0728 REMARK 3 S TENSOR REMARK 3 S11: 0.2104 S12: 0.0399 S13: 0.0057 REMARK 3 S21: -0.1109 S22: 0.0229 S23: 0.7076 REMARK 3 S31: -0.1554 S32: -1.3451 S33: -0.1661 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 245 THROUGH 264 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.9417 -10.4321 -2.3730 REMARK 3 T TENSOR REMARK 3 T11: 0.2996 T22: 0.3407 REMARK 3 T33: 0.1918 T12: -0.0237 REMARK 3 T13: 0.0435 T23: 0.0624 REMARK 3 L TENSOR REMARK 3 L11: 4.4187 L22: 4.7417 REMARK 3 L33: 2.3315 L12: -0.5918 REMARK 3 L13: 0.1392 L23: 2.2986 REMARK 3 S TENSOR REMARK 3 S11: -0.0065 S12: 0.5991 S13: 0.2659 REMARK 3 S21: -0.2261 S22: 0.1172 S23: -0.0264 REMARK 3 S31: -0.4285 S32: 0.0597 S33: -0.1395 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 265 THROUGH 278 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.6461 -30.2402 -12.8786 REMARK 3 T TENSOR REMARK 3 T11: 0.6329 T22: 0.8075 REMARK 3 T33: 0.6450 T12: -0.3686 REMARK 3 T13: 0.0705 T23: -0.3646 REMARK 3 L TENSOR REMARK 3 L11: 2.6134 L22: 0.6633 REMARK 3 L33: 0.6424 L12: -0.2805 REMARK 3 L13: 1.2595 L23: -0.2870 REMARK 3 S TENSOR REMARK 3 S11: -0.0173 S12: 1.0842 S13: -1.1846 REMARK 3 S21: -0.3332 S22: 0.1649 S23: 0.3047 REMARK 3 S31: 0.9667 S32: -0.5049 S33: -0.3959 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 209 THROUGH 223 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.6075 -27.7064 -21.7509 REMARK 3 T TENSOR REMARK 3 T11: 0.7493 T22: 0.8213 REMARK 3 T33: 0.5327 T12: -0.0557 REMARK 3 T13: 0.0507 T23: -0.2102 REMARK 3 L TENSOR REMARK 3 L11: 3.1366 L22: 4.0879 REMARK 3 L33: 4.1356 L12: 0.2716 REMARK 3 L13: -1.4519 L23: -3.8770 REMARK 3 S TENSOR REMARK 3 S11: 0.1193 S12: 0.8908 S13: -0.7858 REMARK 3 S21: -1.3190 S22: -0.4183 S23: 0.0179 REMARK 3 S31: 1.8994 S32: -0.1679 S33: 0.2071 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 224 THROUGH 264 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.5477 -14.0209 -21.6483 REMARK 3 T TENSOR REMARK 3 T11: 0.3605 T22: 0.8021 REMARK 3 T33: 0.3459 T12: 0.0526 REMARK 3 T13: 0.0478 T23: 0.0396 REMARK 3 L TENSOR REMARK 3 L11: 2.3207 L22: 4.4423 REMARK 3 L33: 6.8775 L12: 3.0881 REMARK 3 L13: -2.0983 L23: -1.4919 REMARK 3 S TENSOR REMARK 3 S11: -0.1992 S12: 1.0326 S13: 0.0402 REMARK 3 S21: -0.5574 S22: -0.2509 S23: -0.0473 REMARK 3 S31: 0.3378 S32: -0.1367 S33: 0.4625 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 265 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2332 -31.6899 -11.1875 REMARK 3 T TENSOR REMARK 3 T11: 0.8323 T22: 0.4901 REMARK 3 T33: 0.5953 T12: -0.0747 REMARK 3 T13: 0.2641 T23: -0.1701 REMARK 3 L TENSOR REMARK 3 L11: 4.8761 L22: 6.4568 REMARK 3 L33: 5.3011 L12: -1.5690 REMARK 3 L13: 2.8180 L23: 3.7694 REMARK 3 S TENSOR REMARK 3 S11: -0.2760 S12: 0.6186 S13: -1.4350 REMARK 3 S21: -0.4294 S22: 0.3263 S23: -0.2901 REMARK 3 S31: 1.7263 S32: 0.3674 S33: -0.0713 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 9YE9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000300375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000020 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46470 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 41.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.15970 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M POTASSIUM CHLORIDE, 0.1 M PIPES, 20 % V/V PEG SMEAR MEDIUM, REMARK 280 PH 7.0, 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 29.04050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.41700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.56900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.41700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.04050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.56900 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 29.04050 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -29.56900 REMARK 350 BIOMT3 2 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 B 199 REMARK 465 ALA B 200 REMARK 465 MET B 201 REMARK 465 GLY B 202 REMARK 465 SER B 203 REMARK 465 LYS B 204 REMARK 465 LYS B 205 REMARK 465 ARG B 206 REMARK 465 TRP B 280 REMARK 465 VAL B 281 REMARK 465 GLU B 282 REMARK 465 ASP B 283 REMARK 465 TYR B 284 REMARK 465 GLY C 199 REMARK 465 ALA C 200 REMARK 465 MET C 201 REMARK 465 GLY C 202 REMARK 465 SER C 203 REMARK 465 LYS C 204 REMARK 465 LYS C 205 REMARK 465 ARG C 206 REMARK 465 GLU C 207 REMARK 465 ILE C 208 REMARK 465 ASN C 278 REMARK 465 GLY C 279 REMARK 465 TRP C 280 REMARK 465 VAL C 281 REMARK 465 GLU C 282 REMARK 465 ASP C 283 REMARK 465 TYR C 284 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 GLU B 277 CG CD OE1 OE2 REMARK 470 LYS C 236 CG CD CE NZ REMARK 470 ARG C 244 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 276 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 107 S2 BME A 202 2.03 REMARK 500 SG CYS A 111 S2 BME A 203 2.03 REMARK 500 SG CYS C 225 S2 BME C 302 2.03 REMARK 500 SG CYS B 225 S2 BME B 302 2.03 REMARK 500 SG CYS A 21 S2 BME A 201 2.03 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 90 -104.44 -120.55 REMARK 500 ASN A 114 68.81 -109.99 REMARK 500 ASP A 130 71.79 -151.36 REMARK 500 VAL B 245 -62.73 -99.44 REMARK 500 ARG B 253 -7.44 76.40 REMARK 500 ASN B 278 -122.21 -129.38 REMARK 500 ILE C 216 -56.90 -127.74 REMARK 500 GLN C 276 37.13 -73.36 REMARK 500 REMARK 500 REMARK: NULL DBREF 9YE9 A 1 147 UNP P62837 UB2D2_HUMAN 1 147 DBREF 9YE9 B 204 284 UNP F6NGW2 F6NGW2_DANRE 204 284 DBREF 9YE9 C 204 284 UNP F6NGW2 F6NGW2_DANRE 204 284 SEQADV 9YE9 GLY A -4 UNP P62837 EXPRESSION TAG SEQADV 9YE9 ALA A -3 UNP P62837 EXPRESSION TAG SEQADV 9YE9 MET A -2 UNP P62837 EXPRESSION TAG SEQADV 9YE9 GLY A -1 UNP P62837 EXPRESSION TAG SEQADV 9YE9 SER A 0 UNP P62837 EXPRESSION TAG SEQADV 9YE9 LYS A 1 UNP P62837 MET 1 ENGINEERED MUTATION SEQADV 9YE9 LYS A 85 UNP P62837 CYS 85 ENGINEERED MUTATION SEQADV 9YE9 GLY B 199 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 ALA B 200 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 MET B 201 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 GLY B 202 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 SER B 203 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 GLY C 199 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 ALA C 200 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 MET C 201 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 GLY C 202 UNP F6NGW2 EXPRESSION TAG SEQADV 9YE9 SER C 203 UNP F6NGW2 EXPRESSION TAG SEQRES 1 A 152 GLY ALA MET GLY SER LYS ALA LEU LYS ARG ILE HIS LYS SEQRES 2 A 152 GLU LEU ASN ASP LEU ALA ARG ASP PRO PRO ALA GLN CYS SEQRES 3 A 152 SER ALA GLY PRO VAL GLY ASP ASP MET PHE HIS TRP GLN SEQRES 4 A 152 ALA THR ILE MET GLY PRO ASN ASP SER PRO TYR GLN GLY SEQRES 5 A 152 GLY VAL PHE PHE LEU THR ILE HIS PHE PRO THR ASP TYR SEQRES 6 A 152 PRO PHE LYS PRO PRO LYS VAL ALA PHE THR THR ARG ILE SEQRES 7 A 152 TYR HIS PRO ASN ILE ASN SER ASN GLY SER ILE LYS LEU SEQRES 8 A 152 ASP ILE LEU ARG SER GLN TRP SER PRO ALA LEU THR ILE SEQRES 9 A 152 SER LYS VAL LEU LEU SER ILE CYS SER LEU LEU CYS ASP SEQRES 10 A 152 PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU ILE ALA ARG SEQRES 11 A 152 ILE TYR LYS THR ASP ARG GLU LYS TYR ASN ARG ILE ALA SEQRES 12 A 152 ARG GLU TRP THR GLN LYS TYR ALA MET SEQRES 1 B 86 GLY ALA MET GLY SER LYS LYS ARG GLU ILE PRO ASP TYR SEQRES 2 B 86 LEU CYS GLY LYS ILE SER PHE GLU LEU MET ARG GLU PRO SEQRES 3 B 86 CYS ILE THR PRO SER GLY ILE THR TYR ASP ARG LYS ASP SEQRES 4 B 86 ILE GLU GLU HIS LEU GLN ARG VAL GLY HIS PHE ASP PRO SEQRES 5 B 86 VAL THR ARG SER PRO LEU THR GLN ASP GLN LEU ILE PRO SEQRES 6 B 86 ASN LEU ALA MET LYS GLU VAL ILE ASP ALA PHE ILE GLN SEQRES 7 B 86 GLU ASN GLY TRP VAL GLU ASP TYR SEQRES 1 C 86 GLY ALA MET GLY SER LYS LYS ARG GLU ILE PRO ASP TYR SEQRES 2 C 86 LEU CYS GLY LYS ILE SER PHE GLU LEU MET ARG GLU PRO SEQRES 3 C 86 CYS ILE THR PRO SER GLY ILE THR TYR ASP ARG LYS ASP SEQRES 4 C 86 ILE GLU GLU HIS LEU GLN ARG VAL GLY HIS PHE ASP PRO SEQRES 5 C 86 VAL THR ARG SER PRO LEU THR GLN ASP GLN LEU ILE PRO SEQRES 6 C 86 ASN LEU ALA MET LYS GLU VAL ILE ASP ALA PHE ILE GLN SEQRES 7 C 86 GLU ASN GLY TRP VAL GLU ASP TYR HET BME A 201 4 HET BME A 202 4 HET BME A 203 4 HET CL B 301 1 HET BME B 302 4 HET CL C 301 1 HET BME C 302 4 HETNAM BME BETA-MERCAPTOETHANOL HETNAM CL CHLORIDE ION FORMUL 4 BME 5(C2 H6 O S) FORMUL 7 CL 2(CL 1-) FORMUL 11 HOH *143(H2 O) HELIX 1 AA1 GLY A -4 ASP A 16 1 21 HELIX 2 AA2 LEU A 86 ARG A 90 5 5 HELIX 3 AA3 THR A 98 ASP A 112 1 15 HELIX 4 AA4 VAL A 120 ASP A 130 1 11 HELIX 5 AA5 ASP A 130 ALA A 146 1 17 HELIX 6 AA6 PRO B 209 CYS B 213 5 5 HELIX 7 AA7 ARG B 235 VAL B 245 1 11 HELIX 8 AA8 THR B 257 LEU B 261 5 5 HELIX 9 AA9 ASN B 264 GLN B 276 1 13 HELIX 10 AB1 PRO C 209 CYS C 213 5 5 HELIX 11 AB2 ARG C 235 VAL C 245 1 11 HELIX 12 AB3 THR C 257 LEU C 261 5 5 HELIX 13 AB4 ASN C 264 GLN C 276 1 13 SHEET 1 AA1 4 CYS A 21 PRO A 25 0 SHEET 2 AA1 4 HIS A 32 MET A 38 -1 O THR A 36 N SER A 22 SHEET 3 AA1 4 VAL A 49 HIS A 55 -1 O PHE A 50 N ILE A 37 SHEET 4 AA1 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 SHEET 1 AA2 3 THR B 232 ASP B 234 0 SHEET 2 AA2 3 PRO B 224 ILE B 226 -1 N CYS B 225 O TYR B 233 SHEET 3 AA2 3 ILE B 262 PRO B 263 -1 O ILE B 262 N ILE B 226 SHEET 1 AA3 3 THR C 232 ASP C 234 0 SHEET 2 AA3 3 PRO C 224 ILE C 226 -1 N CYS C 225 O TYR C 233 SHEET 3 AA3 3 ILE C 262 PRO C 263 -1 O ILE C 262 N ILE C 226 CISPEP 1 TYR A 60 PRO A 61 0 8.81 CRYST1 58.081 59.138 112.834 90.00 90.00 90.00 P 21 21 21 8 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 0.017217 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016910 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008863 0.00000 CONECT 2334 2335 2336 CONECT 2335 2334 2337 CONECT 2336 2334 CONECT 2337 2335 CONECT 2338 2339 2340 CONECT 2339 2338 2341 CONECT 2340 2338 CONECT 2341 2339 CONECT 2342 2343 2344 CONECT 2343 2342 2345 CONECT 2344 2342 CONECT 2345 2343 CONECT 2347 2348 2349 CONECT 2348 2347 2350 CONECT 2349 2347 CONECT 2350 2348 CONECT 2352 2353 2354 CONECT 2353 2352 2355 CONECT 2354 2352 CONECT 2355 2353 MASTER 563 0 7 13 10 0 0 6 2495 3 20 26 END