HEADER VIRAL PROTEIN 10-JUL-23 8TFD TITLE CRYSTAL STRUCTURE OF A STEM-LOOP DNA APTAMER COMPLEXED WITH SARS-COV-2 TITLE 2 NUCLEOCAPSID PROTEIN RNA-BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N,NUCLEOCAPSID PROTEIN,NC,PROTEIN N; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA APTAMER; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS DNA BINDING PROTEIN, ENDONUCLEASE, REPLICATION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.ESLER,C.BELICA,K.SHI,H.AIHARA REVDAT 2 11-DEC-24 8TFD 1 JRNL REVDAT 1 13-NOV-24 8TFD 0 JRNL AUTH M.A.ESLER,C.A.BELICA,J.A.ROLLIE,W.L.BROWN,S.A.MOGHADASI, JRNL AUTH 2 K.SHI,D.A.HARKI,R.S.HARRIS,H.AIHARA JRNL TITL A COMPACT STEM-LOOP DNA APTAMER TARGETS A URACIL-BINDING JRNL TITL 2 POCKET IN THE SARS-COV-2 NUCLEOCAPSID RNA-BINDING DOMAIN. JRNL REF NUCLEIC ACIDS RES. V. 52 13138 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 39380503 JRNL DOI 10.1093/NAR/GKAE874 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 27749 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1438 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 47.4800 - 3.3400 1.00 3040 166 0.1349 0.1641 REMARK 3 2 3.3400 - 2.6500 1.00 2901 154 0.1521 0.1816 REMARK 3 3 2.6500 - 2.3200 1.00 2861 169 0.1646 0.1730 REMARK 3 4 2.3200 - 2.1000 1.00 2838 160 0.1627 0.2141 REMARK 3 5 2.1000 - 1.9500 1.00 2852 155 0.1857 0.2256 REMARK 3 6 1.9500 - 1.8400 1.00 2823 158 0.1771 0.1791 REMARK 3 7 1.8400 - 1.7500 0.99 2781 152 0.1683 0.2044 REMARK 3 8 1.7500 - 1.6700 0.89 2562 109 0.1925 0.2604 REMARK 3 9 1.6700 - 1.6100 0.75 2090 125 0.2375 0.2832 REMARK 3 10 1.6100 - 1.5500 0.55 1563 90 0.3466 0.3434 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.75 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 : 0.015 1492 REMARK 3 ANGLE : 1.413 2100 REMARK 3 CHIRALITY : 0.085 220 REMARK 3 PLANARITY : 0.016 204 REMARK 3 DIHEDRAL : 21.236 574 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 47 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1626 -3.4706 33.3427 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.1814 REMARK 3 T33: 0.1736 T12: 0.0071 REMARK 3 T13: 0.0541 T23: -0.0293 REMARK 3 L TENSOR REMARK 3 L11: 3.9866 L22: 4.0875 REMARK 3 L33: 6.3511 L12: -1.1664 REMARK 3 L13: -0.0376 L23: 1.4428 REMARK 3 S TENSOR REMARK 3 S11: 0.0396 S12: -0.4237 S13: 0.5658 REMARK 3 S21: 0.5423 S22: 0.0039 S23: 0.3768 REMARK 3 S31: -0.3312 S32: -0.4551 S33: 0.0503 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 57 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.3369 -0.4952 18.6575 REMARK 3 T TENSOR REMARK 3 T11: 0.1947 T22: 0.2102 REMARK 3 T33: 0.2133 T12: -0.0371 REMARK 3 T13: 0.0422 T23: 0.0193 REMARK 3 L TENSOR REMARK 3 L11: 7.2382 L22: 5.5043 REMARK 3 L33: 2.6461 L12: 2.2878 REMARK 3 L13: 1.2119 L23: 1.1613 REMARK 3 S TENSOR REMARK 3 S11: -0.2761 S12: 0.6182 S13: 0.1376 REMARK 3 S21: -0.5286 S22: 0.1653 S23: -0.4493 REMARK 3 S31: -0.0793 S32: 0.4322 S33: 0.0259 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.5801 -6.8575 21.4043 REMARK 3 T TENSOR REMARK 3 T11: 0.0889 T22: 0.1274 REMARK 3 T33: 0.0984 T12: 0.0083 REMARK 3 T13: 0.0095 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 4.2282 L22: 4.0045 REMARK 3 L33: 2.7487 L12: 1.2320 REMARK 3 L13: 0.9480 L23: 0.5203 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: -0.0134 S13: -0.1061 REMARK 3 S21: 0.0033 S22: -0.0400 S23: 0.2801 REMARK 3 S31: 0.1563 S32: -0.2082 S33: 0.0577 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6519 8.4126 36.3755 REMARK 3 T TENSOR REMARK 3 T11: 0.1798 T22: 0.2685 REMARK 3 T33: 0.2751 T12: -0.0115 REMARK 3 T13: -0.0342 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 2.6144 L22: 4.0589 REMARK 3 L33: 5.8809 L12: -0.5284 REMARK 3 L13: 2.2756 L23: -0.9194 REMARK 3 S TENSOR REMARK 3 S11: -0.1119 S12: -0.1963 S13: -0.0643 REMARK 3 S21: 0.3044 S22: -0.0408 S23: -0.5832 REMARK 3 S31: -0.2088 S32: 0.6423 S33: 0.0333 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 101 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9162 1.6602 28.4070 REMARK 3 T TENSOR REMARK 3 T11: 0.1493 T22: 0.1381 REMARK 3 T33: 0.1325 T12: 0.0191 REMARK 3 T13: 0.0026 T23: 0.0189 REMARK 3 L TENSOR REMARK 3 L11: 8.8450 L22: 6.4467 REMARK 3 L33: 1.5857 L12: 6.9499 REMARK 3 L13: 2.9959 L23: 2.5380 REMARK 3 S TENSOR REMARK 3 S11: -0.0454 S12: 0.0007 S13: -0.1043 REMARK 3 S21: 0.0066 S22: 0.0330 S23: -0.2764 REMARK 3 S31: -0.0321 S32: 0.0309 S33: -0.0052 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.4469 5.5274 21.6365 REMARK 3 T TENSOR REMARK 3 T11: 0.1916 T22: 0.1306 REMARK 3 T33: 0.2328 T12: 0.0216 REMARK 3 T13: -0.0306 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 4.2631 L22: 0.1842 REMARK 3 L33: 1.0157 L12: -0.6051 REMARK 3 L13: 1.0520 L23: -0.0361 REMARK 3 S TENSOR REMARK 3 S11: -0.2555 S12: 0.0674 S13: 0.3251 REMARK 3 S21: -0.0635 S22: 0.0477 S23: -0.0748 REMARK 3 S31: -0.1816 S32: -0.1129 S33: 0.1803 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 139 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.7776 -3.6018 16.4387 REMARK 3 T TENSOR REMARK 3 T11: 0.1020 T22: 0.1522 REMARK 3 T33: 0.1324 T12: 0.0058 REMARK 3 T13: -0.0060 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 4.4718 L22: 7.4361 REMARK 3 L33: 3.7018 L12: 5.5660 REMARK 3 L13: 3.0513 L23: 2.9043 REMARK 3 S TENSOR REMARK 3 S11: -0.1620 S12: 0.1082 S13: 0.1003 REMARK 3 S21: -0.2274 S22: 0.1032 S23: 0.1633 REMARK 3 S31: -0.0863 S32: -0.1870 S33: 0.0111 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 140 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.4034 -5.9067 32.2300 REMARK 3 T TENSOR REMARK 3 T11: 0.1694 T22: 0.2360 REMARK 3 T33: 0.1788 T12: -0.0341 REMARK 3 T13: 0.0479 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 1.5952 L22: 0.6450 REMARK 3 L33: 5.3068 L12: -0.2542 REMARK 3 L13: 2.1577 L23: -0.5849 REMARK 3 S TENSOR REMARK 3 S11: -0.0801 S12: -0.4837 S13: -0.0486 REMARK 3 S21: 0.1638 S22: 0.0176 S23: 0.2715 REMARK 3 S31: 0.0085 S32: -0.8682 S33: 0.0039 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 160 THROUGH 173 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2574 -10.2413 18.5129 REMARK 3 T TENSOR REMARK 3 T11: 0.1448 T22: 0.1617 REMARK 3 T33: 0.2619 T12: -0.0096 REMARK 3 T13: 0.0301 T23: -0.0373 REMARK 3 L TENSOR REMARK 3 L11: 3.2430 L22: 2.3910 REMARK 3 L33: 0.6798 L12: 2.0562 REMARK 3 L13: -0.8332 L23: 0.1820 REMARK 3 S TENSOR REMARK 3 S11: 0.0355 S12: 0.0711 S13: -0.0844 REMARK 3 S21: -0.0473 S22: 0.1601 S23: -0.7208 REMARK 3 S31: 0.0017 S32: 0.3790 S33: -0.1221 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3733 0.4340 53.3609 REMARK 3 T TENSOR REMARK 3 T11: 0.5389 T22: 0.6275 REMARK 3 T33: 0.3946 T12: 0.0145 REMARK 3 T13: 0.0613 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 5.0590 L22: 3.4609 REMARK 3 L33: 7.2525 L12: -1.0290 REMARK 3 L13: -3.7094 L23: -3.0832 REMARK 3 S TENSOR REMARK 3 S11: 0.8853 S12: 0.8934 S13: 0.7574 REMARK 3 S21: -0.8017 S22: -0.1381 S23: 0.6205 REMARK 3 S31: 0.1879 S32: -0.9892 S33: -0.5848 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 6 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6534 -1.8883 40.0817 REMARK 3 T TENSOR REMARK 3 T11: 0.2300 T22: 0.2206 REMARK 3 T33: 0.1529 T12: 0.0205 REMARK 3 T13: -0.0035 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 2.4674 L22: 2.1204 REMARK 3 L33: 2.9531 L12: -0.0046 REMARK 3 L13: 2.3548 L23: -0.6250 REMARK 3 S TENSOR REMARK 3 S11: 0.0487 S12: -0.1050 S13: -0.1507 REMARK 3 S21: 0.2143 S22: -0.0062 S23: -0.0973 REMARK 3 S31: 0.1779 S32: 0.1144 S33: -0.0167 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.7666 -3.5951 55.8826 REMARK 3 T TENSOR REMARK 3 T11: 0.4653 T22: 0.3525 REMARK 3 T33: 0.2342 T12: 0.0825 REMARK 3 T13: 0.0560 T23: 0.0600 REMARK 3 L TENSOR REMARK 3 L11: 5.0987 L22: 4.6314 REMARK 3 L33: 6.2254 L12: -4.7178 REMARK 3 L13: -5.5151 L23: 5.1347 REMARK 3 S TENSOR REMARK 3 S11: -0.1416 S12: -0.3000 S13: 0.1275 REMARK 3 S21: 0.2012 S22: 0.1117 S23: -0.3749 REMARK 3 S31: 1.2826 S32: 0.6144 S33: 0.0526 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 8TFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000275831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27808 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 54.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 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 (%): 50.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM FORMATE,10% W/V REMARK 280 POLYVINYLPYRROLIDONE, 20% W/V PEG 4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K 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 18.89750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.40650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.06650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.40650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.89750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.06650 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: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 45 REMARK 465 PRO A 46 REMARK 465 GLU A 174 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 68 NE 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 O2 EDO A 205 O HOH A 301 1.81 REMARK 500 O HOH A 301 O HOH B 254 1.86 REMARK 500 OH TYR A 172 O HOH A 302 2.07 REMARK 500 O HOH A 309 O HOH B 239 2.09 REMARK 500 O HOH A 423 O HOH A 433 2.16 REMARK 500 O HOH A 351 O HOH A 429 2.17 REMARK 500 NH1 ARG A 68 O HOH A 303 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 303 O HOH B 265 2454 2.07 REMARK 500 O HOH A 376 O HOH A 436 3545 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DT B 8 O3' DT B 8 C3' -0.042 REMARK 500 DT B 16 O3' DT B 16 C3' -0.036 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC B 2 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 7 O3' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES 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 ASN A 75 110.90 -164.21 REMARK 500 LYS A 143 59.56 -92.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 92 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8TFD A 46 174 UNP P0DTC9 NCAP_SARS2 46 174 DBREF 8TFD B 1 20 PDB 8TFD 8TFD 1 20 SEQADV 8TFD GLY A 45 UNP P0DTC9 EXPRESSION TAG SEQRES 1 A 130 GLY PRO ASN ASN THR ALA SER TRP PHE THR ALA LEU THR SEQRES 2 A 130 GLN HIS GLY LYS GLU ASP LEU LYS PHE PRO ARG GLY GLN SEQRES 3 A 130 GLY VAL PRO ILE ASN THR ASN SER SER PRO ASP ASP GLN SEQRES 4 A 130 ILE GLY TYR TYR ARG ARG ALA THR ARG ARG ILE ARG GLY SEQRES 5 A 130 GLY ASP GLY LYS MET LYS ASP LEU SER PRO ARG TRP TYR SEQRES 6 A 130 PHE TYR TYR LEU GLY THR GLY PRO GLU ALA GLY LEU PRO SEQRES 7 A 130 TYR GLY ALA ASN LYS ASP GLY ILE ILE TRP VAL ALA THR SEQRES 8 A 130 GLU GLY ALA LEU ASN THR PRO LYS ASP HIS ILE GLY THR SEQRES 9 A 130 ARG ASN PRO ALA ASN ASN ALA ALA ILE VAL LEU GLN LEU SEQRES 10 A 130 PRO GLN GLY THR THR LEU PRO LYS GLY PHE TYR ALA GLU SEQRES 1 B 20 DT DC DG DG DA DC DA DT DC DG DG DA DT SEQRES 2 B 20 DT DG DT DC DT DG DA 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 B 101 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 6(C2 H6 O2) FORMUL 9 HOH *249(H2 O) HELIX 1 AA1 SER A 79 ASP A 82 5 4 HELIX 2 AA2 THR A 115 ALA A 119 5 5 SHEET 1 AA1 4 LEU A 56 THR A 57 0 SHEET 2 AA1 4 ARG A 107 TYR A 112 -1 O TRP A 108 N LEU A 56 SHEET 3 AA1 4 ILE A 84 ALA A 90 -1 N TYR A 86 O TYR A 111 SHEET 4 AA1 4 ILE A 130 ALA A 134 -1 O VAL A 133 N GLY A 85 SHEET 1 AA2 2 ARG A 93 ARG A 95 0 SHEET 2 AA2 2 MET A 101 ASP A 103 -1 O LYS A 102 N ILE A 94 CRYST1 37.795 54.133 98.813 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.026459 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018473 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010120 0.00000 CONECT 1400 1401 1402 CONECT 1401 1400 CONECT 1402 1400 1403 CONECT 1403 1402 CONECT 1404 1405 1406 CONECT 1405 1404 CONECT 1406 1404 1407 CONECT 1407 1406 CONECT 1408 1409 1410 CONECT 1409 1408 CONECT 1410 1408 1411 CONECT 1411 1410 CONECT 1412 1413 1414 CONECT 1413 1412 CONECT 1414 1412 1415 CONECT 1415 1414 CONECT 1416 1417 1418 CONECT 1417 1416 CONECT 1418 1416 1419 CONECT 1419 1418 CONECT 1420 1421 1422 CONECT 1421 1420 CONECT 1422 1420 1423 CONECT 1423 1422 MASTER 513 0 6 2 6 0 0 6 1670 2 24 12 END