HEADER VIRAL PROTEIN 30-SEP-20 7KAG TITLE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE DOMAIN 1 (UBL1) OF NSP3 FROM TITLE 2 SARS-COV-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN; COMPND 5 SYNONYM: NSP3,PL2-PRO,PAPAIN-LIKE PROTEASE,PAPAIN-LIKE PROTEINASE,PL- COMPND 6 PRO; COMPND 7 EC: 3.4.19.121, 3.4.22.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMCSG53YP_009725299 KEYWDS VIRAL PROTEIN, SARS-COV-2, NON-STRUCTURAL PROTEIN, NSP3, UBIQUITIN- KEYWDS 2 LIKE DOMAIN, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF KEYWDS 3 INFECTIOUS DISEASES, CSGID, NATIONAL INSTITUTE OF ALLERGY AND KEYWDS 4 INFECTIOUS DISEASES, NIAID EXPDTA X-RAY DIFFRACTION AUTHOR P.J.STOGIOS,T.SKARINA,C.CHANG,Y.KIM,R.DI LEO,A.SAVCHENKO, AUTHOR 2 A.JOACHIMIAK,K.J.F.SATCHELL,CENTER FOR STRUCTURAL GENOMICS OF AUTHOR 3 INFECTIOUS DISEASES (CSGID) REVDAT 4 18-OCT-23 7KAG 1 REMARK REVDAT 3 26-JAN-22 7KAG 1 REMARK SEQRES REVDAT 2 27-JAN-21 7KAG 1 COMPND REVDAT 1 14-OCT-20 7KAG 0 JRNL AUTH P.J.STOGIOS JRNL TITL CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE DOMAIN 1 (UBL1) OF JRNL TITL 2 NSP3 FROM SARS-COV-2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3448 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) : 3.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.5 REMARK 3 NUMBER OF REFLECTIONS : 8008 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 793 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 35.7800 - 5.8200 0.95 1594 176 0.2072 0.2357 REMARK 3 2 5.8200 - 4.6300 0.96 1594 175 0.1978 0.2176 REMARK 3 3 4.6300 - 4.0400 0.97 1600 176 0.1949 0.2469 REMARK 3 4 4.0400 - 3.6700 0.86 1423 159 0.2386 0.2626 REMARK 3 5 3.6700 - 3.4100 0.46 769 81 0.2503 0.2850 REMARK 3 6 3.4100 - 3.2100 0.14 235 26 0.3261 0.4250 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) : 0.383 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.80 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 : 0.002 1831 REMARK 3 ANGLE : 0.512 2468 REMARK 3 CHIRALITY : 0.041 282 REMARK 3 PLANARITY : 0.004 312 REMARK 3 DIHEDRAL : 16.780 653 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 20 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.7414 72.4932 6.2646 REMARK 3 T TENSOR REMARK 3 T11: 0.2427 T22: 0.5093 REMARK 3 T33: 0.6675 T12: 0.0662 REMARK 3 T13: 0.1675 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 3.8603 L22: 2.6796 REMARK 3 L33: 8.3996 L12: -0.5680 REMARK 3 L13: -3.8529 L23: -0.3209 REMARK 3 S TENSOR REMARK 3 S11: 0.0834 S12: -1.5508 S13: 0.2224 REMARK 3 S21: 0.4309 S22: 0.5887 S23: 0.5037 REMARK 3 S31: -0.2985 S32: 0.7012 S33: -0.6288 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.3400 61.8353 -0.9189 REMARK 3 T TENSOR REMARK 3 T11: 0.5611 T22: 0.8956 REMARK 3 T33: 1.3714 T12: -0.1783 REMARK 3 T13: 0.1628 T23: -0.1139 REMARK 3 L TENSOR REMARK 3 L11: 6.1083 L22: 4.8017 REMARK 3 L33: 7.4077 L12: -5.3719 REMARK 3 L13: -5.8361 L23: 5.5094 REMARK 3 S TENSOR REMARK 3 S11: -0.0883 S12: -0.3729 S13: -4.0698 REMARK 3 S21: 1.5252 S22: -1.7906 S23: 1.8984 REMARK 3 S31: 1.7896 S32: -1.2034 S33: 1.8613 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.8516 70.9112 4.9939 REMARK 3 T TENSOR REMARK 3 T11: 0.4172 T22: 0.3061 REMARK 3 T33: 0.4846 T12: -0.0035 REMARK 3 T13: 0.1590 T23: 0.1980 REMARK 3 L TENSOR REMARK 3 L11: 5.9052 L22: 4.0428 REMARK 3 L33: 5.5226 L12: 4.2404 REMARK 3 L13: 0.5680 L23: 2.7447 REMARK 3 S TENSOR REMARK 3 S11: 0.6772 S12: -0.1509 S13: 0.9424 REMARK 3 S21: 1.2414 S22: -0.4333 S23: 0.5099 REMARK 3 S31: -0.0937 S32: -0.2375 S33: -0.3030 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.9160 96.7304 12.5745 REMARK 3 T TENSOR REMARK 3 T11: 0.5409 T22: 0.1510 REMARK 3 T33: 0.4934 T12: -0.0640 REMARK 3 T13: -0.0694 T23: -0.0842 REMARK 3 L TENSOR REMARK 3 L11: 0.7845 L22: 1.6508 REMARK 3 L33: 1.2487 L12: -0.9285 REMARK 3 L13: -0.1061 L23: -0.6993 REMARK 3 S TENSOR REMARK 3 S11: -0.3213 S12: -0.0173 S13: -0.0436 REMARK 3 S21: -0.1472 S22: 0.0273 S23: -0.1457 REMARK 3 S31: -0.5717 S32: 0.0275 S33: 0.0074 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 30 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.7229 93.6709 15.0675 REMARK 3 T TENSOR REMARK 3 T11: 0.2976 T22: 0.1403 REMARK 3 T33: 0.5340 T12: -0.0735 REMARK 3 T13: 0.1381 T23: -0.0314 REMARK 3 L TENSOR REMARK 3 L11: 4.3249 L22: 5.5924 REMARK 3 L33: 3.9005 L12: 2.6445 REMARK 3 L13: 1.8171 L23: 2.7611 REMARK 3 S TENSOR REMARK 3 S11: -0.2037 S12: 0.1616 S13: -0.3047 REMARK 3 S21: -0.0036 S22: -0.2515 S23: 0.4507 REMARK 3 S31: -0.0023 S32: -0.1661 S33: 0.2229 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 50 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.8537 93.3481 19.4112 REMARK 3 T TENSOR REMARK 3 T11: 0.2806 T22: 0.4886 REMARK 3 T33: 0.8514 T12: -0.1041 REMARK 3 T13: -0.0553 T23: -0.1235 REMARK 3 L TENSOR REMARK 3 L11: 2.6026 L22: 1.0864 REMARK 3 L33: 7.0804 L12: 0.6834 REMARK 3 L13: 4.2796 L23: 1.3153 REMARK 3 S TENSOR REMARK 3 S11: 0.5468 S12: -1.0292 S13: -0.3344 REMARK 3 S21: -0.1103 S22: -0.4347 S23: 0.7542 REMARK 3 S31: 0.6721 S32: -1.7283 S33: -0.1644 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 63 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.0402 99.2980 30.5197 REMARK 3 T TENSOR REMARK 3 T11: 0.4840 T22: 0.2284 REMARK 3 T33: 0.4803 T12: 0.1508 REMARK 3 T13: -0.1308 T23: -0.1152 REMARK 3 L TENSOR REMARK 3 L11: 2.4340 L22: 2.0001 REMARK 3 L33: 4.4653 L12: 2.8451 REMARK 3 L13: 3.2638 L23: 4.5910 REMARK 3 S TENSOR REMARK 3 S11: -0.0482 S12: -0.4309 S13: 0.0033 REMARK 3 S21: 1.4096 S22: 0.0409 S23: 0.5721 REMARK 3 S31: 0.4062 S32: -0.1322 S33: -0.0093 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.1900 101.1257 27.6807 REMARK 3 T TENSOR REMARK 3 T11: 0.4484 T22: 0.6318 REMARK 3 T33: 0.5539 T12: 0.2303 REMARK 3 T13: 0.0405 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 9.9993 L22: 7.7608 REMARK 3 L33: 5.3021 L12: 2.7411 REMARK 3 L13: 7.2610 L23: 2.4468 REMARK 3 S TENSOR REMARK 3 S11: -0.3316 S12: -1.2476 S13: 0.7202 REMARK 3 S21: 0.7835 S22: 0.0661 S23: 1.6410 REMARK 3 S31: -1.0206 S32: -2.4392 S33: 0.1980 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.4444 101.6516 9.9673 REMARK 3 T TENSOR REMARK 3 T11: 0.9316 T22: 0.4898 REMARK 3 T33: 0.7476 T12: 0.0525 REMARK 3 T13: -0.1747 T23: -0.3144 REMARK 3 L TENSOR REMARK 3 L11: 5.9151 L22: 4.0407 REMARK 3 L33: 5.5680 L12: 3.5025 REMARK 3 L13: -0.3053 L23: 0.8100 REMARK 3 S TENSOR REMARK 3 S11: -0.7774 S12: 0.8431 S13: -0.2849 REMARK 3 S21: -1.2498 S22: -0.1250 S23: 0.6860 REMARK 3 S31: 0.5067 S32: -1.1541 S33: 0.9046 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 97 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1148 101.5996 5.9923 REMARK 3 T TENSOR REMARK 3 T11: 0.8679 T22: 0.9922 REMARK 3 T33: 1.2017 T12: 0.0866 REMARK 3 T13: -0.5621 T23: -0.1492 REMARK 3 L TENSOR REMARK 3 L11: 8.7069 L22: 3.6411 REMARK 3 L33: 5.1959 L12: 5.6262 REMARK 3 L13: 1.4882 L23: 0.7973 REMARK 3 S TENSOR REMARK 3 S11: 0.2491 S12: -0.0742 S13: -1.0179 REMARK 3 S21: -0.9235 S22: 0.5580 S23: 0.6034 REMARK 3 S31: 0.9698 S32: -2.4690 S33: -0.7369 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 98 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.8075 97.6081 8.1945 REMARK 3 T TENSOR REMARK 3 T11: 0.5342 T22: 0.2203 REMARK 3 T33: 0.5815 T12: 0.0430 REMARK 3 T13: -0.2206 T23: 0.0688 REMARK 3 L TENSOR REMARK 3 L11: 4.0641 L22: 5.2824 REMARK 3 L33: 5.5527 L12: 1.9345 REMARK 3 L13: 2.5584 L23: 5.1198 REMARK 3 S TENSOR REMARK 3 S11: -0.2168 S12: 0.3615 S13: 0.1151 REMARK 3 S21: -0.5592 S22: -0.0736 S23: 0.5283 REMARK 3 S31: -0.5829 S32: 0.2260 S33: 0.2491 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.8497 108.8152 14.3033 REMARK 3 T TENSOR REMARK 3 T11: 1.2024 T22: 0.5826 REMARK 3 T33: 1.3483 T12: 0.3298 REMARK 3 T13: -0.4078 T23: -0.2573 REMARK 3 L TENSOR REMARK 3 L11: 5.7526 L22: 7.1521 REMARK 3 L33: 1.3213 L12: -0.5636 REMARK 3 L13: -0.7118 L23: -2.8571 REMARK 3 S TENSOR REMARK 3 S11: 0.4668 S12: 0.6224 S13: 0.5360 REMARK 3 S21: -2.3035 S22: -0.2698 S23: 2.4029 REMARK 3 S31: -1.0325 S32: -0.8095 S33: -0.1919 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.4514 80.0934 -2.2323 REMARK 3 T TENSOR REMARK 3 T11: 0.3243 T22: 0.6122 REMARK 3 T33: 0.6210 T12: 0.2311 REMARK 3 T13: -0.1888 T23: 0.1029 REMARK 3 L TENSOR REMARK 3 L11: 4.3692 L22: 3.2274 REMARK 3 L33: 4.5149 L12: 0.9467 REMARK 3 L13: 2.4719 L23: 1.3160 REMARK 3 S TENSOR REMARK 3 S11: -0.0884 S12: 0.1008 S13: 0.2350 REMARK 3 S21: -0.2097 S22: -0.1597 S23: 0.3285 REMARK 3 S31: -0.4114 S32: -0.3044 S33: 0.0462 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 12 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.0688 63.9834 -7.2573 REMARK 3 T TENSOR REMARK 3 T11: 0.2050 T22: 0.3334 REMARK 3 T33: 0.5566 T12: 0.0862 REMARK 3 T13: 0.1295 T23: -0.0838 REMARK 3 L TENSOR REMARK 3 L11: 0.3781 L22: 3.6185 REMARK 3 L33: 1.1793 L12: -0.4126 REMARK 3 L13: -0.3233 L23: 0.7063 REMARK 3 S TENSOR REMARK 3 S11: 0.2379 S12: 0.4238 S13: 0.0885 REMARK 3 S21: -0.1854 S22: -0.3388 S23: -0.1050 REMARK 3 S31: 0.1232 S32: 0.1988 S33: 0.2808 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 25 THROUGH 31 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.2048 41.9029 -19.1289 REMARK 3 T TENSOR REMARK 3 T11: 0.8212 T22: 0.1363 REMARK 3 T33: 0.4900 T12: 0.0888 REMARK 3 T13: 0.1196 T23: 0.0417 REMARK 3 L TENSOR REMARK 3 L11: 2.9742 L22: 1.7419 REMARK 3 L33: 2.2789 L12: -2.0567 REMARK 3 L13: -2.3951 L23: 1.9905 REMARK 3 S TENSOR REMARK 3 S11: -0.2233 S12: -0.1001 S13: -0.4359 REMARK 3 S21: 0.2731 S22: -0.0066 S23: 0.0883 REMARK 3 S31: 0.5745 S32: 0.1035 S33: 0.0750 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 32 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.4688 53.9895 -16.8569 REMARK 3 T TENSOR REMARK 3 T11: 0.2754 T22: 0.1556 REMARK 3 T33: 0.5913 T12: -0.0275 REMARK 3 T13: -0.1534 T23: -0.0825 REMARK 3 L TENSOR REMARK 3 L11: 0.0857 L22: 2.3069 REMARK 3 L33: 2.5880 L12: 0.4401 REMARK 3 L13: 0.2858 L23: 1.6039 REMARK 3 S TENSOR REMARK 3 S11: -0.1756 S12: 0.0042 S13: 0.1719 REMARK 3 S21: -0.0914 S22: -0.4359 S23: 0.5636 REMARK 3 S31: -0.2416 S32: -0.4383 S33: 0.1079 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 65 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.8698 45.9809 -31.1621 REMARK 3 T TENSOR REMARK 3 T11: 0.5594 T22: 0.3374 REMARK 3 T33: 0.4326 T12: -0.1437 REMARK 3 T13: 0.1172 T23: -0.1545 REMARK 3 L TENSOR REMARK 3 L11: 3.4257 L22: 9.4716 REMARK 3 L33: 5.4357 L12: -3.1761 REMARK 3 L13: -2.1471 L23: 2.5209 REMARK 3 S TENSOR REMARK 3 S11: -0.1850 S12: 0.4582 S13: 0.0540 REMARK 3 S21: -1.4022 S22: -0.3861 S23: 0.3873 REMARK 3 S31: 0.0307 S32: -0.7803 S33: 0.4139 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 79 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.5018 45.0443 -23.6592 REMARK 3 T TENSOR REMARK 3 T11: 0.6110 T22: 0.5210 REMARK 3 T33: 0.7195 T12: -0.3025 REMARK 3 T13: -0.0702 T23: -0.1088 REMARK 3 L TENSOR REMARK 3 L11: 8.9579 L22: 4.0398 REMARK 3 L33: 0.8618 L12: 2.2803 REMARK 3 L13: -2.4192 L23: -1.4646 REMARK 3 S TENSOR REMARK 3 S11: -0.5295 S12: 1.2610 S13: -0.1702 REMARK 3 S21: -0.5572 S22: 0.1258 S23: 0.9527 REMARK 3 S31: 1.1020 S32: -1.4143 S33: 0.3014 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 91 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.7376 46.9723 -5.5482 REMARK 3 T TENSOR REMARK 3 T11: 0.7271 T22: 0.7492 REMARK 3 T33: 1.0451 T12: -0.0666 REMARK 3 T13: 0.4942 T23: -0.1767 REMARK 3 L TENSOR REMARK 3 L11: 4.6715 L22: 3.2687 REMARK 3 L33: 1.0741 L12: -2.4656 REMARK 3 L13: 1.8945 L23: -1.0368 REMARK 3 S TENSOR REMARK 3 S11: -0.7874 S12: 0.0777 S13: -1.5974 REMARK 3 S21: 0.0608 S22: 0.8198 S23: -0.2788 REMARK 3 S31: 0.2065 S32: -0.8014 S33: 0.0731 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.9332 41.2431 -12.5955 REMARK 3 T TENSOR REMARK 3 T11: 0.8723 T22: 0.4626 REMARK 3 T33: 0.9774 T12: -0.1473 REMARK 3 T13: 0.4415 T23: 0.0362 REMARK 3 L TENSOR REMARK 3 L11: 4.2360 L22: 0.7978 REMARK 3 L33: 6.2134 L12: 0.8130 REMARK 3 L13: 3.2217 L23: -0.9358 REMARK 3 S TENSOR REMARK 3 S11: 0.0247 S12: -0.3578 S13: -1.7041 REMARK 3 S21: 0.4674 S22: 0.0307 S23: -0.0566 REMARK 3 S31: 1.0722 S32: -0.9603 S33: -0.1625 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 7KAG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10868 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.130 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.93300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2GRI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 82.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 0.1 M HEPES PH REMARK 280 7.5, 2% HEXANEDIOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.91500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 73.78500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.91500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 73.78500 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: 3150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 81.83000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 303 LIES ON A SPECIAL POSITION. 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 PHE A 7 30.69 -98.49 REMARK 500 ASP A 9 -114.60 52.60 REMARK 500 ARG A 30 -41.64 -134.77 REMARK 500 CYS A 39 44.59 -154.57 REMARK 500 ASP A 110 -126.39 61.80 REMARK 500 ASP B 9 -115.13 52.30 REMARK 500 GLU B 29 -2.76 58.90 REMARK 500 CYS B 39 47.03 -142.91 REMARK 500 VAL B 68 48.15 -101.46 REMARK 500 ASP B 110 -140.35 58.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 208 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CSGID-IDP52003 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 7TI9 RELATED DB: PDB DBREF 7KAG A 1 111 UNP P0DTD1 R1AB_SARS2 819 929 DBREF 7KAG B 1 111 UNP P0DTD1 R1AB_SARS2 819 929 SEQRES 1 A 111 ALA PRO THR LYS VAL THR PHE GLY ASP ASP THR VAL ILE SEQRES 2 A 111 GLU VAL GLN GLY TYR LYS SER VAL ASN ILE THR PHE GLU SEQRES 3 A 111 LEU ASP GLU ARG ILE ASP LYS VAL LEU ASN GLU LYS CYS SEQRES 4 A 111 SER ALA TYR THR VAL GLU LEU GLY THR GLU VAL ASN GLU SEQRES 5 A 111 PHE ALA CYS VAL VAL ALA ASP ALA VAL ILE LYS THR LEU SEQRES 6 A 111 GLN PRO VAL SER GLU LEU LEU THR PRO LEU GLY ILE ASP SEQRES 7 A 111 LEU ASP GLU TRP SER MET ALA THR TYR TYR LEU PHE ASP SEQRES 8 A 111 GLU SER GLY GLU PHE LYS LEU ALA SER HIS MET TYR CYS SEQRES 9 A 111 SER PHE TYR PRO PRO ASP GLU SEQRES 1 B 111 ALA PRO THR LYS VAL THR PHE GLY ASP ASP THR VAL ILE SEQRES 2 B 111 GLU VAL GLN GLY TYR LYS SER VAL ASN ILE THR PHE GLU SEQRES 3 B 111 LEU ASP GLU ARG ILE ASP LYS VAL LEU ASN GLU LYS CYS SEQRES 4 B 111 SER ALA TYR THR VAL GLU LEU GLY THR GLU VAL ASN GLU SEQRES 5 B 111 PHE ALA CYS VAL VAL ALA ASP ALA VAL ILE LYS THR LEU SEQRES 6 B 111 GLN PRO VAL SER GLU LEU LEU THR PRO LEU GLY ILE ASP SEQRES 7 B 111 LEU ASP GLU TRP SER MET ALA THR TYR TYR LEU PHE ASP SEQRES 8 B 111 GLU SER GLY GLU PHE LYS LEU ALA SER HIS MET TYR CYS SEQRES 9 B 111 SER PHE TYR PRO PRO ASP GLU HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HET EDO B 201 4 HET EDO B 202 4 HET EDO B 203 4 HET SO4 B 204 5 HET EDO B 205 4 HET EDO B 206 4 HET EDO B 207 4 HET EDO B 208 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 13(C2 H6 O2) FORMUL 12 SO4 O4 S 2- FORMUL 17 HOH *22(H2 O) HELIX 1 AA1 ILE A 31 CYS A 39 1 9 HELIX 2 AA2 GLU A 49 GLN A 66 1 18 HELIX 3 AA3 VAL A 68 THR A 73 1 6 HELIX 4 AA4 ASP A 78 SER A 83 1 6 HELIX 5 AA5 ILE B 31 CYS B 39 1 9 HELIX 6 AA6 GLU B 49 GLN B 66 1 18 HELIX 7 AA7 ASP B 78 SER B 83 1 6 SHEET 1 AA1 2 THR A 3 THR A 6 0 SHEET 2 AA1 2 VAL A 12 VAL A 15 -1 O ILE A 13 N VAL A 5 SHEET 1 AA2 4 ALA A 41 GLU A 45 0 SHEET 2 AA2 4 TYR A 18 PHE A 25 -1 N VAL A 21 O TYR A 42 SHEET 3 AA2 4 HIS A 101 SER A 105 1 O MET A 102 N THR A 24 SHEET 4 AA2 4 TYR A 88 PHE A 90 -1 N TYR A 88 O SER A 105 SHEET 1 AA3 2 THR B 3 THR B 6 0 SHEET 2 AA3 2 VAL B 12 VAL B 15 -1 O ILE B 13 N VAL B 5 SHEET 1 AA4 4 ALA B 41 GLU B 45 0 SHEET 2 AA4 4 TYR B 18 PHE B 25 -1 N LYS B 19 O VAL B 44 SHEET 3 AA4 4 HIS B 101 SER B 105 1 O MET B 102 N THR B 24 SHEET 4 AA4 4 TYR B 88 PHE B 90 -1 N TYR B 88 O SER B 105 SITE 1 AC1 3 LYS A 19 LEU A 98 ASP B 10 SITE 1 AC2 2 TRP A 82 ALA A 85 SITE 1 AC3 2 PHE A 90 ASP A 110 SITE 1 AC4 4 PRO A 67 VAL A 68 SER A 69 GLU A 70 SITE 1 AC5 2 ASP A 28 THR B 73 SITE 1 AC6 2 GLN A 16 GLU B 14 SITE 1 AC7 1 GLU B 26 SITE 1 AC8 1 TRP B 82 SITE 1 AC9 5 ASP A 9 ASP A 10 LYS B 19 ALA B 99 SITE 2 AC9 5 SER B 100 SITE 1 AD1 1 PRO B 67 SITE 1 AD2 3 THR A 73 ASP B 28 GLU B 29 SITE 1 AD3 2 ALA B 85 TYR B 87 SITE 1 AD4 1 TYR B 42 CRYST1 81.830 147.570 70.137 90.00 125.90 90.00 C 1 2 1 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 0.012220 0.000000 0.008845 0.00000 SCALE2 0.000000 0.006776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017600 0.00000