HEADER VIRAL PROTEIN 28-OCT-21 7Q3Q TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RBD IN COMPLEX WITH THE NEUTRALIZING TITLE 2 NANOBODY VHH-12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VHH-12; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_TAXID: 30538; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 8 2; SOURCE 9 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 10 ORGANISM_TAXID: 2697049; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS CORONAVIRUS, NANOBODY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.FERNANDEZ,R.PEDERZOLI,F.A.REY REVDAT 2 31-JAN-24 7Q3Q 1 REMARK REVDAT 1 16-NOV-22 7Q3Q 0 JRNL AUTH I.FERNANDEZ,F.A.REY JRNL TITL NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN JRNL TITL 2 AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 20002 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1018 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 47.4100 - 4.4000 1.00 2968 134 0.1619 0.1594 REMARK 3 2 4.4000 - 3.4900 1.00 2745 148 0.1600 0.2000 REMARK 3 3 3.4900 - 3.0500 0.99 2707 150 0.1925 0.2289 REMARK 3 4 3.0500 - 2.7700 0.99 2653 160 0.2180 0.3241 REMARK 3 5 2.7700 - 2.5700 0.99 2666 134 0.2362 0.2916 REMARK 3 6 2.5700 - 2.4200 0.99 2626 147 0.2283 0.2543 REMARK 3 7 2.4200 - 2.3000 0.99 2619 145 0.2827 0.3391 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.81 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 : 15 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.2387 -0.0860 -18.4795 REMARK 3 T TENSOR REMARK 3 T11: 0.8536 T22: 0.6512 REMARK 3 T33: 0.8379 T12: -0.2141 REMARK 3 T13: -0.2729 T23: 0.1029 REMARK 3 L TENSOR REMARK 3 L11: 5.6174 L22: 5.5503 REMARK 3 L33: 2.9983 L12: -5.3938 REMARK 3 L13: 0.7972 L23: 0.2671 REMARK 3 S TENSOR REMARK 3 S11: -1.4638 S12: -0.3055 S13: 2.4025 REMARK 3 S21: 1.0859 S22: -0.0808 S23: -2.3537 REMARK 3 S31: -2.6090 S32: 1.1902 S33: 1.5901 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 10 THROUGH 19 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7189 -17.6494 -4.7263 REMARK 3 T TENSOR REMARK 3 T11: 0.4371 T22: 0.6870 REMARK 3 T33: 0.4729 T12: -0.0806 REMARK 3 T13: -0.1433 T23: 0.1372 REMARK 3 L TENSOR REMARK 3 L11: 5.7771 L22: 5.5183 REMARK 3 L33: 7.3913 L12: 5.6419 REMARK 3 L13: -6.3878 L23: -6.3273 REMARK 3 S TENSOR REMARK 3 S11: 0.2709 S12: -0.5769 S13: -0.3907 REMARK 3 S21: -0.0798 S22: -0.8282 S23: -0.7658 REMARK 3 S31: 0.1396 S32: 1.2591 S33: 0.4951 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 20 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2815 -5.4854 -16.1012 REMARK 3 T TENSOR REMARK 3 T11: 0.5678 T22: 0.4565 REMARK 3 T33: 0.4229 T12: -0.0243 REMARK 3 T13: -0.1176 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 5.3084 L22: 9.0799 REMARK 3 L33: 7.4095 L12: -5.4028 REMARK 3 L13: 5.8586 L23: -4.2246 REMARK 3 S TENSOR REMARK 3 S11: -0.9386 S12: -0.7542 S13: 0.8298 REMARK 3 S21: 0.1419 S22: 0.2161 S23: -0.2588 REMARK 3 S31: -1.0248 S32: -0.2914 S33: 0.6700 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 36 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8646 -16.0933 -21.8285 REMARK 3 T TENSOR REMARK 3 T11: 0.4847 T22: 0.8315 REMARK 3 T33: 0.4504 T12: -0.0682 REMARK 3 T13: -0.0061 T23: 0.0266 REMARK 3 L TENSOR REMARK 3 L11: 8.8555 L22: 2.3258 REMARK 3 L33: 6.0025 L12: -4.3156 REMARK 3 L13: -2.7920 L23: 1.7279 REMARK 3 S TENSOR REMARK 3 S11: 0.0528 S12: 0.7240 S13: 0.5531 REMARK 3 S21: -0.9332 S22: 0.1627 S23: -0.4389 REMARK 3 S31: -0.4630 S32: 1.3206 S33: -0.1823 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 48 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.3161 -16.6039 -20.3435 REMARK 3 T TENSOR REMARK 3 T11: 0.4231 T22: 0.3647 REMARK 3 T33: 0.3711 T12: -0.0363 REMARK 3 T13: -0.1105 T23: 0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.3706 L22: 7.7453 REMARK 3 L33: 6.6141 L12: 0.1466 REMARK 3 L13: -1.4144 L23: -0.4441 REMARK 3 S TENSOR REMARK 3 S11: 0.2972 S12: -0.1978 S13: -0.4836 REMARK 3 S21: 0.1880 S22: -0.2099 S23: 0.1720 REMARK 3 S31: 0.3534 S32: -0.0316 S33: -0.1390 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 63 THROUGH 85 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.1938 -14.8954 -12.1203 REMARK 3 T TENSOR REMARK 3 T11: 0.4767 T22: 0.3871 REMARK 3 T33: 0.3597 T12: -0.0300 REMARK 3 T13: -0.0514 T23: 0.0564 REMARK 3 L TENSOR REMARK 3 L11: 9.0453 L22: 4.3578 REMARK 3 L33: 4.9838 L12: -5.6179 REMARK 3 L13: 4.2072 L23: -4.2373 REMARK 3 S TENSOR REMARK 3 S11: -0.2990 S12: -0.6706 S13: -0.2016 REMARK 3 S21: 0.7253 S22: 0.3995 S23: 0.2530 REMARK 3 S31: -0.2128 S32: -0.1593 S33: -0.0803 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 86 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.0854 -18.0026 -14.2201 REMARK 3 T TENSOR REMARK 3 T11: 0.4382 T22: 0.5516 REMARK 3 T33: 0.4243 T12: 0.0086 REMARK 3 T13: -0.0743 T23: 0.0348 REMARK 3 L TENSOR REMARK 3 L11: 3.3143 L22: 7.9735 REMARK 3 L33: 3.9717 L12: -4.5494 REMARK 3 L13: 3.4193 L23: -3.9636 REMARK 3 S TENSOR REMARK 3 S11: 0.2875 S12: 0.4176 S13: -0.4289 REMARK 3 S21: -0.8493 S22: -0.1769 S23: 0.2476 REMARK 3 S31: 0.3114 S32: 0.4611 S33: 0.0744 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9497 -12.3994 -28.2853 REMARK 3 T TENSOR REMARK 3 T11: 0.4753 T22: 0.4290 REMARK 3 T33: 0.3661 T12: -0.0025 REMARK 3 T13: -0.1016 T23: 0.0809 REMARK 3 L TENSOR REMARK 3 L11: 6.5443 L22: 3.6272 REMARK 3 L33: 4.3768 L12: 0.6249 REMARK 3 L13: -0.4906 L23: 3.8154 REMARK 3 S TENSOR REMARK 3 S11: 0.0593 S12: 0.9517 S13: 0.5783 REMARK 3 S21: -0.4675 S22: -0.4466 S23: -0.2250 REMARK 3 S31: -0.8084 S32: 0.5819 S33: 0.3599 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 113 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2328 -11.0677 -20.6668 REMARK 3 T TENSOR REMARK 3 T11: 0.4211 T22: 0.5768 REMARK 3 T33: 0.3327 T12: -0.0418 REMARK 3 T13: -0.0002 T23: 0.0713 REMARK 3 L TENSOR REMARK 3 L11: 7.8549 L22: 5.8141 REMARK 3 L33: 4.4473 L12: -2.7437 REMARK 3 L13: 5.9402 L23: -2.2461 REMARK 3 S TENSOR REMARK 3 S11: -0.6711 S12: 0.3154 S13: 0.0648 REMARK 3 S21: 0.1666 S22: 0.2737 S23: -0.0766 REMARK 3 S31: -0.8615 S32: 0.8131 S33: 0.5763 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 334 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.2693 -8.3820 -43.3441 REMARK 3 T TENSOR REMARK 3 T11: 0.5678 T22: 0.4693 REMARK 3 T33: 0.4664 T12: 0.1108 REMARK 3 T13: -0.0795 T23: -0.1502 REMARK 3 L TENSOR REMARK 3 L11: 5.4755 L22: 2.7070 REMARK 3 L33: 1.7507 L12: 0.1282 REMARK 3 L13: 2.2749 L23: -0.1683 REMARK 3 S TENSOR REMARK 3 S11: -0.1586 S12: -0.3050 S13: 0.5451 REMARK 3 S21: 0.0298 S22: -0.1974 S23: 0.3155 REMARK 3 S31: -0.4253 S32: -0.3586 S33: 0.3837 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 365 THROUGH 375 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.8266 -3.3717 -56.7015 REMARK 3 T TENSOR REMARK 3 T11: 0.9643 T22: 0.4911 REMARK 3 T33: 0.5508 T12: 0.0165 REMARK 3 T13: -0.0748 T23: 0.0865 REMARK 3 L TENSOR REMARK 3 L11: 4.3062 L22: 9.4162 REMARK 3 L33: 6.3784 L12: 6.3514 REMARK 3 L13: 4.9202 L23: 7.1679 REMARK 3 S TENSOR REMARK 3 S11: -0.4404 S12: 0.6354 S13: 1.5533 REMARK 3 S21: -0.9850 S22: 0.3665 S23: 0.6512 REMARK 3 S31: -2.0187 S32: 0.0742 S33: 0.1501 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 376 THROUGH 421 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.4656 -16.1719 -51.2713 REMARK 3 T TENSOR REMARK 3 T11: 0.5415 T22: 0.2768 REMARK 3 T33: 0.4107 T12: 0.0441 REMARK 3 T13: -0.0647 T23: -0.0650 REMARK 3 L TENSOR REMARK 3 L11: 6.5319 L22: 0.5909 REMARK 3 L33: 4.5994 L12: 0.0541 REMARK 3 L13: 2.3295 L23: -0.2076 REMARK 3 S TENSOR REMARK 3 S11: 0.2004 S12: 0.3975 S13: -0.0298 REMARK 3 S21: -0.2485 S22: -0.1085 S23: 0.0148 REMARK 3 S31: -0.0463 S32: 0.1227 S33: -0.0986 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 422 THROUGH 494 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.6788 -18.9481 -36.3459 REMARK 3 T TENSOR REMARK 3 T11: 0.3874 T22: 0.3046 REMARK 3 T33: 0.3614 T12: 0.0074 REMARK 3 T13: -0.0223 T23: -0.0311 REMARK 3 L TENSOR REMARK 3 L11: 2.8579 L22: 0.6215 REMARK 3 L33: 6.0909 L12: -0.7150 REMARK 3 L13: 3.1938 L23: -0.8264 REMARK 3 S TENSOR REMARK 3 S11: 0.2070 S12: -0.0174 S13: -0.2926 REMARK 3 S21: -0.1623 S22: -0.1111 S23: 0.0631 REMARK 3 S31: 0.3081 S32: -0.0954 S33: -0.1387 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 495 THROUGH 506 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7672 -5.3621 -43.2240 REMARK 3 T TENSOR REMARK 3 T11: 0.5222 T22: 0.4785 REMARK 3 T33: 0.5697 T12: -0.0757 REMARK 3 T13: -0.1050 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 5.2244 L22: 5.1098 REMARK 3 L33: 7.1749 L12: 5.1693 REMARK 3 L13: -5.5740 L23: -5.4936 REMARK 3 S TENSOR REMARK 3 S11: 0.1925 S12: -0.5340 S13: 0.0007 REMARK 3 S21: 0.2914 S22: -0.0183 S23: -0.9397 REMARK 3 S31: -0.1335 S32: 0.5026 S33: -0.0184 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 507 THROUGH 526 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.4617 -14.9559 -49.7158 REMARK 3 T TENSOR REMARK 3 T11: 0.5002 T22: 0.4260 REMARK 3 T33: 0.4366 T12: 0.0842 REMARK 3 T13: -0.1628 T23: -0.0453 REMARK 3 L TENSOR REMARK 3 L11: 6.5229 L22: 5.3418 REMARK 3 L33: 2.0502 L12: 5.9541 REMARK 3 L13: 3.4569 L23: 3.2550 REMARK 3 S TENSOR REMARK 3 S11: 0.3591 S12: 0.0284 S13: -0.1475 REMARK 3 S21: -0.0448 S22: -0.2967 S23: 0.1820 REMARK 3 S31: 0.0214 S32: -0.1352 S33: -0.0127 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 7Q3Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292118922. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980112 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20030 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 47.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 52.10 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 55.20 REMARK 200 R MERGE FOR SHELL (I) : 1.76100 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: PHENIX REMARK 200 STARTING MODEL: 6YM0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1 M TRIS-HCL (PH 8.5) REMARK 280 AND 0.2 M LI2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 109.26250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.22550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.22550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 163.89375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.22550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.22550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.63125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.22550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.22550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 163.89375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.22550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.22550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.63125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 109.26250 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: B, A, 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 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 A 757 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 ALA B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 130 REMARK 465 ALA B 131 REMARK 465 ALA B 132 REMARK 465 HIS B 133 REMARK 465 HIS B 134 REMARK 465 HIS B 135 REMARK 465 HIS B 136 REMARK 465 HIS B 137 REMARK 465 HIS B 138 REMARK 465 HIS B 139 REMARK 465 HIS B 140 REMARK 465 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 LYS A 528 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 ALA A 352 50.34 -111.08 REMARK 500 ASN A 422 -53.94 -127.11 REMARK 500 ASP A 428 30.79 -91.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Q3Q B 0 140 PDB 7Q3Q 7Q3Q 0 140 DBREF1 7Q3Q A 331 528 UNP A0A6H2EIN2_SARS2 DBREF2 7Q3Q A A0A6H2EIN2 331 528 SEQRES 1 B 141 ALA MET ALA GLU VAL GLN LEU GLN ALA SER GLY GLY GLY SEQRES 2 B 141 LEU VAL GLU ALA GLY GLY SER LEU ARG LEU SER CYS THR SEQRES 3 B 141 THR SER GLY LEU THR PHE SER SER VAL THR MET GLY TRP SEQRES 4 B 141 PHE ARG GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA SEQRES 5 B 141 ALA ILE ARG TRP LYS PHE GLY ASN LEU GLY TYR ALA ASP SEQRES 6 B 141 SER VAL LYS GLY ARG PHE THR VAL SER ARG ASP ASN ALA SEQRES 7 B 141 LYS ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO SEQRES 8 B 141 GLU ASP THR ALA VAL TYR TYR CYS ALA ALA ALA ARG VAL SEQRES 9 B 141 GLY GLU ILE ILE ALA VAL LEU ILE SER PRO SER ASN TYR SEQRES 10 B 141 ALA TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 11 B 141 ALA ALA ALA HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 A 198 ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN SEQRES 2 A 198 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 3 A 198 ARG ILE SER ASN CYS VAL ALA ASP TYR SER PHE LEU TYR SEQRES 4 A 198 ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SEQRES 5 A 198 SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL SEQRES 6 A 198 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 7 A 198 GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR SEQRES 8 A 198 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 9 A 198 ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY SEQRES 10 A 198 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 11 A 198 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 12 A 198 GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE SEQRES 13 A 198 ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO SEQRES 14 A 198 THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL SEQRES 15 A 198 LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS SEQRES 16 A 198 GLY PRO LYS HET NAG C 1 14 HET NAG C 2 14 HET CL B 201 1 HET CL B 202 1 HET GOL A 601 6 HET GOL A 602 6 HET GOL A 603 6 HET CL A 604 1 HET SO4 A 605 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 4 CL 3(CL 1-) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 10 SO4 O4 S 2- FORMUL 11 HOH *134(H2 O) HELIX 1 AA1 THR B 30 VAL B 34 5 5 HELIX 2 AA2 LYS B 89 THR B 93 5 5 HELIX 3 AA3 SER B 112 TYR B 116 5 5 HELIX 4 AA4 PRO A 337 ASN A 343 1 7 HELIX 5 AA5 TYR A 365 ASN A 370 1 6 HELIX 6 AA6 SER A 383 ASP A 389 5 7 HELIX 7 AA7 ASP A 405 ILE A 410 5 6 HELIX 8 AA8 GLY A 416 ASN A 422 1 7 HELIX 9 AA9 SER A 438 SER A 443 1 6 HELIX 10 AB1 GLY A 502 TYR A 505 5 4 SHEET 1 AA1 4 GLN B 5 SER B 9 0 SHEET 2 AA1 4 LEU B 20 SER B 27 -1 O THR B 25 N GLN B 7 SHEET 3 AA1 4 THR B 80 MET B 85 -1 O MET B 85 N LEU B 20 SHEET 4 AA1 4 PHE B 70 ASP B 75 -1 N ASP B 75 O THR B 80 SHEET 1 AA2 4 GLY B 12 GLU B 15 0 SHEET 2 AA2 4 THR B 123 SER B 128 1 O THR B 126 N GLY B 12 SHEET 3 AA2 4 ALA B 94 ALA B 100 -1 N TYR B 96 O THR B 123 SHEET 4 AA2 4 TYR B 118 TRP B 119 -1 O TYR B 118 N ALA B 100 SHEET 1 AA3 7 GLY B 12 GLU B 15 0 SHEET 2 AA3 7 THR B 123 SER B 128 1 O THR B 126 N GLY B 12 SHEET 3 AA3 7 ALA B 94 ALA B 100 -1 N TYR B 96 O THR B 123 SHEET 4 AA3 7 MET B 36 GLN B 41 -1 N GLN B 41 O VAL B 95 SHEET 5 AA3 7 GLU B 48 ILE B 53 -1 O GLU B 48 N ARG B 40 SHEET 6 AA3 7 LEU B 60 TYR B 62 -1 O GLY B 61 N ALA B 52 SHEET 7 AA3 7 VAL A 483 GLU A 484 1 O GLU A 484 N LEU B 60 SHEET 1 AA4 5 ASN A 354 ILE A 358 0 SHEET 2 AA4 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA4 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA4 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA4 5 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA5 3 CYS A 361 VAL A 362 0 SHEET 2 AA5 3 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 3 AA5 3 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA6 2 LEU A 452 ARG A 454 0 SHEET 2 AA6 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA7 2 TYR A 473 GLN A 474 0 SHEET 2 AA7 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SSBOND 1 CYS B 24 CYS B 98 1555 1555 2.04 SSBOND 2 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 3 CYS A 379 CYS A 432 1555 1555 2.05 SSBOND 4 CYS A 391 CYS A 525 1555 1555 2.04 SSBOND 5 CYS A 480 CYS A 488 1555 1555 2.04 LINK ND2 ASN A 343 C1 NAG C 1 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 CRYST1 62.451 62.451 218.525 90.00 90.00 90.00 P 43 21 2 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 0.016013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004576 0.00000