HEADER LIGASE 27-FEB-23 8GBQ TITLE STRUCTURE OF RNF125 IN COMPLEX WITH UBCH5B 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 MOL_ID: 2; COMPND 12 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF125; COMPND 13 CHAIN: B; COMPND 14 SYNONYM: RING FINGER PROTEIN 125,T-CELL RING ACTIVATION PROTEIN 1, COMPND 15 TRAC-1; COMPND 16 EC: 2.3.2.27; COMPND 17 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RNF125; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN RING E3 LIGASE UBIQUITIN CONJUGATING ENZYME COMPLEX, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.MIDDLETON,C.L.DAY,T.J.FOKKENS REVDAT 3 18-OCT-23 8GBQ 1 JRNL REVDAT 2 16-AUG-23 8GBQ 1 JRNL REVDAT 1 19-JUL-23 8GBQ 0 JRNL AUTH A.J.MIDDLETON,F.M.BARZAK,T.J.FOKKENS,K.NGUYEN,C.L.DAY JRNL TITL ZINC FINGER 1 OF THE RING E3 LIGASE, RNF125, INTERACTS WITH JRNL TITL 2 THE E2 TO ENHANCE UBIQUITYLATION. JRNL REF STRUCTURE V. 31 1208 2023 JRNL REFN ISSN 0969-2126 JRNL PMID 37541247 JRNL DOI 10.1016/J.STR.2023.07.007 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.190 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 59049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2920 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 41.8700 - 4.8000 0.99 2677 143 0.1550 0.1690 REMARK 3 2 4.8000 - 3.8100 1.00 2691 146 0.1480 0.1650 REMARK 3 3 3.8100 - 3.3300 1.00 2670 162 0.1768 0.1891 REMARK 3 4 3.3300 - 3.0300 1.00 2700 122 0.1963 0.1763 REMARK 3 5 3.0200 - 2.8100 1.00 2628 164 0.2063 0.2457 REMARK 3 6 2.8100 - 2.6400 1.00 2766 128 0.2089 0.2461 REMARK 3 7 2.6400 - 2.5100 1.00 2677 157 0.2172 0.2337 REMARK 3 8 2.5100 - 2.4000 1.00 2702 140 0.1963 0.2124 REMARK 3 9 2.4000 - 2.3100 1.00 2692 108 0.1922 0.1996 REMARK 3 10 2.3100 - 2.2300 1.00 2717 134 0.1925 0.2414 REMARK 3 11 2.2300 - 2.1600 1.00 2648 152 0.1920 0.2219 REMARK 3 12 2.1600 - 2.1000 1.00 2752 108 0.1831 0.1897 REMARK 3 13 2.1000 - 2.0400 1.00 2739 114 0.1980 0.2273 REMARK 3 14 2.0400 - 1.9900 1.00 2680 134 0.2033 0.2145 REMARK 3 15 1.9900 - 1.9500 1.00 2625 174 0.2017 0.2458 REMARK 3 16 1.9500 - 1.9100 1.00 2713 150 0.2217 0.2504 REMARK 3 17 1.9100 - 1.8700 1.00 2671 114 0.2310 0.2849 REMARK 3 18 1.8700 - 1.8300 1.00 2718 156 0.2461 0.2668 REMARK 3 19 1.8300 - 1.8000 1.00 2708 136 0.2522 0.2944 REMARK 3 20 1.8000 - 1.7700 1.00 2630 152 0.2494 0.2965 REMARK 3 21 1.7700 - 1.7400 0.84 2325 126 0.3033 0.2915 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.16 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.8225 -14.1767 -23.4329 REMARK 3 T TENSOR REMARK 3 T11: 0.3432 T22: 0.7006 REMARK 3 T33: 0.4528 T12: -0.0331 REMARK 3 T13: -0.0859 T23: 0.0694 REMARK 3 L TENSOR REMARK 3 L11: 2.1736 L22: 7.2312 REMARK 3 L33: 5.3805 L12: -0.8197 REMARK 3 L13: -1.3406 L23: 2.2259 REMARK 3 S TENSOR REMARK 3 S11: 0.0544 S12: 0.9718 S13: 0.4042 REMARK 3 S21: -0.8665 S22: -0.2053 S23: 1.2270 REMARK 3 S31: -0.3433 S32: -0.4126 S33: 0.3005 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 28 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1878 -4.9102 -22.3988 REMARK 3 T TENSOR REMARK 3 T11: 0.6332 T22: 0.7029 REMARK 3 T33: 0.8371 T12: -0.0340 REMARK 3 T13: -0.1451 T23: 0.1962 REMARK 3 L TENSOR REMARK 3 L11: 2.2356 L22: 4.8993 REMARK 3 L33: 6.5170 L12: 3.3382 REMARK 3 L13: 5.2516 L23: 2.9486 REMARK 3 S TENSOR REMARK 3 S11: -0.2218 S12: 0.4180 S13: 1.0252 REMARK 3 S21: -1.1405 S22: -0.3829 S23: 1.3677 REMARK 3 S31: -1.1692 S32: -0.6605 S33: 0.6542 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 29 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.8399 -10.3560 -23.4611 REMARK 3 T TENSOR REMARK 3 T11: 0.3878 T22: 0.4571 REMARK 3 T33: 0.3157 T12: -0.0065 REMARK 3 T13: -0.0552 T23: 0.1429 REMARK 3 L TENSOR REMARK 3 L11: 6.1312 L22: 9.6530 REMARK 3 L33: 8.8469 L12: 2.8235 REMARK 3 L13: 3.5572 L23: 9.0352 REMARK 3 S TENSOR REMARK 3 S11: -0.4352 S12: 0.5668 S13: 0.3503 REMARK 3 S21: -1.0060 S22: -0.0233 S23: -0.1169 REMARK 3 S31: -1.1531 S32: 0.2119 S33: 0.5021 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4586 -10.0398 -15.3320 REMARK 3 T TENSOR REMARK 3 T11: 0.2479 T22: 0.3355 REMARK 3 T33: 0.3142 T12: 0.0401 REMARK 3 T13: -0.0601 T23: 0.0712 REMARK 3 L TENSOR REMARK 3 L11: 4.7130 L22: 5.8357 REMARK 3 L33: 3.3416 L12: 3.6562 REMARK 3 L13: 1.9641 L23: 0.7722 REMARK 3 S TENSOR REMARK 3 S11: -0.4930 S12: 0.4851 S13: 0.5827 REMARK 3 S21: -0.2079 S22: 0.1531 S23: 0.2045 REMARK 3 S31: -0.5252 S32: -0.0974 S33: 0.3016 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 66 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4430 -8.5357 -14.5387 REMARK 3 T TENSOR REMARK 3 T11: 0.3424 T22: 0.4357 REMARK 3 T33: 0.3734 T12: -0.0590 REMARK 3 T13: -0.0101 T23: 0.0889 REMARK 3 L TENSOR REMARK 3 L11: 6.7834 L22: 9.5314 REMARK 3 L33: 2.2405 L12: 7.0236 REMARK 3 L13: 7.3196 L23: 8.5760 REMARK 3 S TENSOR REMARK 3 S11: -0.1748 S12: 0.7423 S13: -0.2245 REMARK 3 S21: -0.4322 S22: 0.2589 S23: -0.6986 REMARK 3 S31: -0.1452 S32: 0.6900 S33: 0.0721 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.5315 -15.8713 -9.0047 REMARK 3 T TENSOR REMARK 3 T11: 0.1692 T22: 0.2103 REMARK 3 T33: 0.2287 T12: 0.0468 REMARK 3 T13: -0.0006 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 6.4595 L22: 5.9726 REMARK 3 L33: 2.1799 L12: 6.2858 REMARK 3 L13: 1.9320 L23: 1.1494 REMARK 3 S TENSOR REMARK 3 S11: -0.0405 S12: -0.1344 S13: -0.1971 REMARK 3 S21: 0.0584 S22: -0.0644 S23: -0.2502 REMARK 3 S31: 0.0201 S32: -0.0311 S33: 0.0672 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.4434 -7.7923 -9.8209 REMARK 3 T TENSOR REMARK 3 T11: 0.2150 T22: 0.2722 REMARK 3 T33: 0.3560 T12: 0.0462 REMARK 3 T13: 0.0048 T23: 0.0495 REMARK 3 L TENSOR REMARK 3 L11: 10.0342 L22: 9.0378 REMARK 3 L33: 8.5106 L12: 6.6101 REMARK 3 L13: 7.0588 L23: 5.8758 REMARK 3 S TENSOR REMARK 3 S11: -0.4614 S12: -0.1303 S13: 0.9882 REMARK 3 S21: -0.0760 S22: -0.0352 S23: 0.9552 REMARK 3 S31: -0.5117 S32: -0.6717 S33: 0.4365 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 112 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.2768 -11.0786 -0.3359 REMARK 3 T TENSOR REMARK 3 T11: 0.4089 T22: 0.3963 REMARK 3 T33: 0.4323 T12: 0.0066 REMARK 3 T13: 0.0004 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 2.0606 L22: 2.0802 REMARK 3 L33: 2.0879 L12: 1.0568 REMARK 3 L13: 2.4440 L23: 4.5658 REMARK 3 S TENSOR REMARK 3 S11: 0.1733 S12: -0.2423 S13: -0.4920 REMARK 3 S21: 0.6310 S22: -0.1223 S23: 0.3840 REMARK 3 S31: 0.2306 S32: -0.7081 S33: -0.0598 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 130 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6636 -6.1246 2.4803 REMARK 3 T TENSOR REMARK 3 T11: 0.2172 T22: 0.1894 REMARK 3 T33: 0.3207 T12: -0.0093 REMARK 3 T13: -0.0351 T23: 0.0354 REMARK 3 L TENSOR REMARK 3 L11: 6.0749 L22: 2.0889 REMARK 3 L33: 8.4051 L12: 4.9865 REMARK 3 L13: 4.7022 L23: 4.7205 REMARK 3 S TENSOR REMARK 3 S11: -0.0293 S12: -0.0444 S13: -0.2479 REMARK 3 S21: 0.1939 S22: 0.1077 S23: -0.1253 REMARK 3 S31: 0.2249 S32: 0.3024 S33: -0.1277 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 131 THROUGH 147 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8291 2.7259 -7.5350 REMARK 3 T TENSOR REMARK 3 T11: 0.3954 T22: 0.2648 REMARK 3 T33: 0.5776 T12: -0.0764 REMARK 3 T13: -0.0605 T23: 0.1057 REMARK 3 L TENSOR REMARK 3 L11: 4.8529 L22: 7.6139 REMARK 3 L33: 7.6530 L12: 0.5447 REMARK 3 L13: 1.7676 L23: -2.4753 REMARK 3 S TENSOR REMARK 3 S11: -0.4448 S12: 0.4598 S13: 1.0629 REMARK 3 S21: -0.7827 S22: 0.2355 S23: -0.0715 REMARK 3 S31: -0.7566 S32: 0.0808 S33: 0.2445 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 34 THROUGH 46 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.3208 -20.6158 -16.7749 REMARK 3 T TENSOR REMARK 3 T11: 0.2263 T22: 0.3569 REMARK 3 T33: 0.2505 T12: 0.0694 REMARK 3 T13: -0.0433 T23: -0.0769 REMARK 3 L TENSOR REMARK 3 L11: 6.7001 L22: 6.0906 REMARK 3 L33: 8.6659 L12: 2.3715 REMARK 3 L13: 1.2589 L23: -5.1285 REMARK 3 S TENSOR REMARK 3 S11: -0.2828 S12: 0.2409 S13: 0.4954 REMARK 3 S21: -0.2420 S22: -0.1155 S23: 0.2805 REMARK 3 S31: -0.1260 S32: -0.3047 S33: 0.4392 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 47 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.6285 -27.4442 -7.9501 REMARK 3 T TENSOR REMARK 3 T11: 0.1749 T22: 0.2986 REMARK 3 T33: 0.2508 T12: 0.0427 REMARK 3 T13: 0.0198 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 2.5103 L22: 6.9626 REMARK 3 L33: 7.7943 L12: -1.2761 REMARK 3 L13: 0.5111 L23: -1.0954 REMARK 3 S TENSOR REMARK 3 S11: -0.0638 S12: -0.2087 S13: -0.0786 REMARK 3 S21: -0.0068 S22: -0.1508 S23: -0.4108 REMARK 3 S31: 0.2011 S32: 0.3184 S33: 0.2480 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 78 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.3963 -31.8005 -4.4324 REMARK 3 T TENSOR REMARK 3 T11: 0.3004 T22: 0.2885 REMARK 3 T33: 0.4034 T12: -0.0109 REMARK 3 T13: 0.0483 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 2.0245 L22: 3.5594 REMARK 3 L33: 9.6619 L12: 0.8705 REMARK 3 L13: 2.0564 L23: 1.1833 REMARK 3 S TENSOR REMARK 3 S11: 0.0002 S12: 0.8893 S13: -1.1312 REMARK 3 S21: -0.0712 S22: 0.0048 S23: -0.1892 REMARK 3 S31: 0.7119 S32: 0.8595 S33: -0.1085 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 87 THROUGH 95 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.4334 -22.4712 -13.3134 REMARK 3 T TENSOR REMARK 3 T11: 0.2980 T22: 0.6376 REMARK 3 T33: 0.4748 T12: 0.0776 REMARK 3 T13: 0.0013 T23: -0.1591 REMARK 3 L TENSOR REMARK 3 L11: 2.0662 L22: 8.4907 REMARK 3 L33: 2.0596 L12: -1.1654 REMARK 3 L13: 0.4079 L23: -6.3191 REMARK 3 S TENSOR REMARK 3 S11: 0.0466 S12: -0.6394 S13: 0.5884 REMARK 3 S21: 0.3562 S22: -0.2476 S23: 1.3073 REMARK 3 S31: -0.5218 S32: -1.3705 S33: 0.0688 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 96 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.5047 -17.8891 -26.6953 REMARK 3 T TENSOR REMARK 3 T11: 0.3896 T22: 0.5768 REMARK 3 T33: 0.4084 T12: 0.0480 REMARK 3 T13: -0.1397 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 4.4503 L22: 8.6350 REMARK 3 L33: 8.6557 L12: 1.0537 REMARK 3 L13: -3.8190 L23: 3.7709 REMARK 3 S TENSOR REMARK 3 S11: -0.1938 S12: 0.4333 S13: 0.4991 REMARK 3 S21: -0.4915 S22: 0.1999 S23: 0.2841 REMARK 3 S31: -0.9395 S32: -0.2964 S33: 0.0500 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 119 THROUGH 126 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.0917 -18.8364 -34.8872 REMARK 3 T TENSOR REMARK 3 T11: 0.6858 T22: 1.0963 REMARK 3 T33: 0.7346 T12: -0.2523 REMARK 3 T13: 0.0622 T23: 0.2061 REMARK 3 L TENSOR REMARK 3 L11: 2.0362 L22: 9.6434 REMARK 3 L33: 6.9517 L12: 0.0175 REMARK 3 L13: 3.3762 L23: -2.3830 REMARK 3 S TENSOR REMARK 3 S11: -0.4150 S12: 1.0819 S13: 0.7025 REMARK 3 S21: -1.1520 S22: -0.8868 S23: -2.5525 REMARK 3 S31: -1.2634 S32: 3.3976 S33: 1.3485 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 8GBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95373 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 48.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 14.70 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 1.26300 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CHES 9.5 20% PEG 8000, PH 9.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.78233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 109.56467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 109.56467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.78233 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 341 LIES ON A SPECIAL POSITION. 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 -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY B 27 REMARK 465 PRO B 28 REMARK 465 LEU B 29 REMARK 465 GLY B 30 REMARK 465 SER B 31 REMARK 465 VAL B 32 REMARK 465 THR B 33 REMARK 465 GLY B 127 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 GLN A 20 19.26 -146.22 REMARK 500 ARG A 90 -108.64 -141.93 REMARK 500 ASN A 114 78.46 -115.36 REMARK 500 ASP A 130 72.80 -151.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 37 SG REMARK 620 2 CYS B 40 SG 111.8 REMARK 620 3 CYS B 57 SG 105.4 106.4 REMARK 620 4 CYS B 60 SG 110.9 108.8 113.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 52 SG REMARK 620 2 HIS B 54 ND1 112.6 REMARK 620 3 CYS B 72 SG 102.9 115.6 REMARK 620 4 CYS B 75 SG 107.8 106.4 111.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 100 SG REMARK 620 2 CYS B 103 SG 110.7 REMARK 620 3 HIS B 115 NE2 102.0 105.0 REMARK 620 4 CYS B 119 SG 119.2 108.7 110.3 REMARK 620 N 1 2 3 DBREF 8GBQ A 1 147 UNP P62837 UB2D2_HUMAN 1 147 DBREF 8GBQ B 32 127 UNP Q96EQ8 RN125_HUMAN 32 127 SEQADV 8GBQ GLY A -4 UNP P62837 EXPRESSION TAG SEQADV 8GBQ PRO A -3 UNP P62837 EXPRESSION TAG SEQADV 8GBQ LEU A -2 UNP P62837 EXPRESSION TAG SEQADV 8GBQ GLY A -1 UNP P62837 EXPRESSION TAG SEQADV 8GBQ SER A 0 UNP P62837 EXPRESSION TAG SEQADV 8GBQ SER A 21 UNP P62837 CYS 21 ENGINEERED MUTATION SEQADV 8GBQ ARG A 22 UNP P62837 SER 22 ENGINEERED MUTATION SEQADV 8GBQ LYS A 85 UNP P62837 CYS 85 ENGINEERED MUTATION SEQADV 8GBQ SER A 107 UNP P62837 CYS 107 ENGINEERED MUTATION SEQADV 8GBQ SER A 111 UNP P62837 CYS 111 ENGINEERED MUTATION SEQADV 8GBQ GLY B 27 UNP Q96EQ8 EXPRESSION TAG SEQADV 8GBQ PRO B 28 UNP Q96EQ8 EXPRESSION TAG SEQADV 8GBQ LEU B 29 UNP Q96EQ8 EXPRESSION TAG SEQADV 8GBQ GLY B 30 UNP Q96EQ8 EXPRESSION TAG SEQADV 8GBQ SER B 31 UNP Q96EQ8 EXPRESSION TAG SEQRES 1 A 152 GLY PRO LEU GLY SER MET ALA LEU LYS ARG ILE HIS LYS SEQRES 2 A 152 GLU LEU ASN ASP LEU ALA ARG ASP PRO PRO ALA GLN SER SEQRES 3 A 152 ARG 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 SER SER LEU LEU SER 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 101 GLY PRO LEU GLY SER VAL THR SER PHE ASP CYS ALA VAL SEQRES 2 B 101 CYS LEU GLU VAL LEU HIS GLN PRO VAL ARG THR ARG CYS SEQRES 3 B 101 GLY HIS VAL PHE CYS ARG SER CYS ILE ALA THR SER LEU SEQRES 4 B 101 LYS ASN ASN LYS TRP THR CYS PRO TYR CYS ARG ALA TYR SEQRES 5 B 101 LEU PRO SER GLU GLY VAL PRO ALA THR ASP VAL ALA LYS SEQRES 6 B 101 ARG MET LYS SER GLU TYR LYS ASN CYS ALA GLU CYS ASP SEQRES 7 B 101 THR LEU VAL CYS LEU SER GLU MET ARG ALA HIS ILE ARG SEQRES 8 B 101 THR CYS GLN LYS TYR ILE ASP LYS TYR GLY HET GOL B 201 6 HET ZN B 202 1 HET ZN B 203 1 HET ZN B 204 1 HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 ZN 3(ZN 2+) FORMUL 7 HOH *152(H2 O) HELIX 1 AA1 MET A 1 ASP A 16 1 16 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 ARG B 58 ASN B 68 1 11 HELIX 7 AA7 ALA B 86 LYS B 94 1 9 HELIX 8 AA8 GLU B 111 CYS B 119 1 9 HELIX 9 AA9 CYS B 119 TYR B 126 1 8 SHEET 1 AA1 4 SER A 21 VAL A 26 0 SHEET 2 AA1 4 ASP A 29 MET A 38 -1 O HIS A 32 N VAL A 26 SHEET 3 AA1 4 VAL A 49 HIS A 55 -1 O LEU A 52 N ALA A 35 SHEET 4 AA1 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 SHEET 1 AA2 3 VAL B 55 CYS B 57 0 SHEET 2 AA2 3 PRO B 47 ARG B 49 -1 N VAL B 48 O PHE B 56 SHEET 3 AA2 3 VAL B 84 PRO B 85 -1 O VAL B 84 N ARG B 49 SHEET 1 AA3 2 TYR B 97 ASN B 99 0 SHEET 2 AA3 2 LEU B 106 CYS B 108 -1 O VAL B 107 N LYS B 98 LINK SG CYS B 37 ZN ZN B 202 1555 1555 2.35 LINK SG CYS B 40 ZN ZN B 202 1555 1555 2.34 LINK SG CYS B 52 ZN ZN B 203 1555 1555 2.27 LINK ND1 HIS B 54 ZN ZN B 203 1555 1555 2.07 LINK SG CYS B 57 ZN ZN B 202 1555 1555 2.36 LINK SG CYS B 60 ZN ZN B 202 1555 1555 2.32 LINK SG CYS B 72 ZN ZN B 203 1555 1555 2.31 LINK SG CYS B 75 ZN ZN B 203 1555 1555 2.33 LINK SG CYS B 100 ZN ZN B 204 1555 1555 2.33 LINK SG CYS B 103 ZN ZN B 204 1555 1555 2.32 LINK NE2 HIS B 115 ZN ZN B 204 1555 1555 2.09 LINK SG CYS B 119 ZN ZN B 204 1555 1555 2.34 CISPEP 1 TYR A 60 PRO A 61 0 6.53 CRYST1 56.181 56.181 164.347 90.00 90.00 120.00 P 31 2 1 6 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 0.017800 0.010277 0.000000 0.00000 SCALE2 0.000000 0.020553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006085 0.00000