HEADER VIRAL PROTEIN 31-AUG-21 7VBE TITLE 1.6 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF SARS-COV-2 NUCLEOCAPSID TITLE 2 DIMERIZATION DOMAIN, PH 5.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN; COMPND 5 SYNONYM: N,NUCLEOCAPSID PROTEIN,NC,PROTEIN N; COMPND 6 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, NUCLEOCAPSID DIMERIZATION DOMAIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.L.ZHOU,F.L.ZHONG,J.LI,J.ZHANG REVDAT 2 29-NOV-23 7VBE 1 REMARK REVDAT 1 06-JUL-22 7VBE 0 JRNL AUTH X.L.ZHOU,F.L.ZHONG,J.LI,J.ZHANG JRNL TITL 1.6 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF SARS-COV-2 JRNL TITL 2 NUCLEOCAPSID DIMERIZATION DOMAIN, PH 5.0 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.344 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 69247 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.417 REMARK 3 FREE R VALUE TEST SET COUNT : 3751 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 29.7800 - 4.7637 0.98 2390 141 0.1679 0.1894 REMARK 3 2 4.7637 - 3.7836 1.00 2451 133 0.1509 0.1659 REMARK 3 3 3.7836 - 3.3060 1.00 2424 134 0.1847 0.2008 REMARK 3 4 3.3060 - 3.0040 1.00 2444 136 0.1892 0.2221 REMARK 3 5 3.0040 - 2.7889 1.00 2434 142 0.1901 0.2050 REMARK 3 6 2.7889 - 2.6246 1.00 2424 139 0.2018 0.2304 REMARK 3 7 2.6246 - 2.4932 1.00 2438 135 0.1973 0.2570 REMARK 3 8 2.4932 - 2.3847 1.00 2405 137 0.2068 0.2259 REMARK 3 9 2.3847 - 2.2929 1.00 2413 140 0.1921 0.2274 REMARK 3 10 2.2929 - 2.2138 1.00 2465 139 0.1971 0.2560 REMARK 3 11 2.2138 - 2.1446 1.00 2421 138 0.2031 0.2390 REMARK 3 12 2.1446 - 2.0834 1.00 2439 140 0.2175 0.2228 REMARK 3 13 2.0834 - 2.0285 1.00 2436 142 0.2160 0.2311 REMARK 3 14 2.0285 - 1.9790 1.00 2386 140 0.2224 0.2293 REMARK 3 15 1.9790 - 1.9341 1.00 2444 140 0.2328 0.2846 REMARK 3 16 1.9341 - 1.8929 1.00 2384 140 0.2374 0.2809 REMARK 3 17 1.8929 - 1.8551 1.00 2471 144 0.2569 0.2677 REMARK 3 18 1.8551 - 1.8200 1.00 2408 143 0.2694 0.3429 REMARK 3 19 1.8200 - 1.7875 1.00 2421 140 0.0000 0.2679 REMARK 3 20 1.7875 - 1.7573 1.00 2425 134 0.0000 0.2509 REMARK 3 21 1.7573 - 1.7289 1.00 2428 137 0.2847 0.3194 REMARK 3 22 1.7289 - 1.7023 1.00 2446 144 0.3010 0.3146 REMARK 3 23 1.7023 - 1.6773 1.00 2391 132 0.3242 0.3473 REMARK 3 24 1.6773 - 1.6537 1.00 2471 143 0.3338 0.3539 REMARK 3 25 1.6537 - 1.6313 1.00 2420 139 0.3400 0.4001 REMARK 3 26 1.6313 - 1.6101 0.99 2382 141 0.0000 0.3182 REMARK 3 27 1.6101 - 1.5900 0.99 2435 138 0.3633 0.3820 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) : 0.237 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.302 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.72 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 : 0.006 1712 REMARK 3 ANGLE : 0.817 2325 REMARK 3 CHIRALITY : 0.056 244 REMARK 3 PLANARITY : 0.007 308 REMARK 3 DIHEDRAL : 14.259 1004 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 7VBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300023029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69247 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 29.783 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 6WJI REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE PH 5.0, 30% V/V POLYETHYLENE GLYCOL MONOMETHYL ETHER REMARK 280 550, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 51.66500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.74500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.66500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.74500 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: 5190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 PRO B 364 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 257 CG CD CE NZ REMARK 470 ARG A 276 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 281 CG CD OE1 NE2 REMARK 470 LYS A 299 CG CD CE NZ REMARK 470 LYS A 342 CG CD CE NZ REMARK 470 LYS B 266 CG CD CE NZ REMARK 470 ARG B 276 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 280 CG CD OE1 OE2 REMARK 470 GLN B 281 CG CD OE1 NE2 REMARK 470 THR B 282 OG1 CG2 REMARK 470 GLN B 289 CG CD OE1 NE2 REMARK 470 ASP B 341 CG OD1 OD2 REMARK 470 LYS B 342 CG CD CE NZ REMARK 470 LYS B 355 CG CD CE NZ 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 NZ LYS B 338 O HOH B 401 2.03 REMARK 500 O GLN A 281 O HOH A 401 2.17 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 TYR A 268 83.87 -150.76 REMARK 500 TYR B 268 82.24 -151.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VBE A 257 364 UNP P0DTC9 NCAP_SARS2 257 364 DBREF 7VBE B 257 364 UNP P0DTC9 NCAP_SARS2 257 364 SEQRES 1 A 108 LYS PRO ARG GLN LYS ARG THR ALA THR LYS ALA TYR ASN SEQRES 2 A 108 VAL THR GLN ALA PHE GLY ARG ARG GLY PRO GLU GLN THR SEQRES 3 A 108 GLN GLY ASN PHE GLY ASP GLN GLU LEU ILE ARG GLN GLY SEQRES 4 A 108 THR ASP TYR LYS HIS TRP PRO GLN ILE ALA GLN PHE ALA SEQRES 5 A 108 PRO SER ALA SER ALA PHE PHE GLY MET SER ARG ILE GLY SEQRES 6 A 108 MET GLU VAL THR PRO SER GLY THR TRP LEU THR TYR THR SEQRES 7 A 108 GLY ALA ILE LYS LEU ASP ASP LYS ASP PRO ASN PHE LYS SEQRES 8 A 108 ASP GLN VAL ILE LEU LEU ASN LYS HIS ILE ASP ALA TYR SEQRES 9 A 108 LYS THR PHE PRO SEQRES 1 B 108 LYS PRO ARG GLN LYS ARG THR ALA THR LYS ALA TYR ASN SEQRES 2 B 108 VAL THR GLN ALA PHE GLY ARG ARG GLY PRO GLU GLN THR SEQRES 3 B 108 GLN GLY ASN PHE GLY ASP GLN GLU LEU ILE ARG GLN GLY SEQRES 4 B 108 THR ASP TYR LYS HIS TRP PRO GLN ILE ALA GLN PHE ALA SEQRES 5 B 108 PRO SER ALA SER ALA PHE PHE GLY MET SER ARG ILE GLY SEQRES 6 B 108 MET GLU VAL THR PRO SER GLY THR TRP LEU THR TYR THR SEQRES 7 B 108 GLY ALA ILE LYS LEU ASP ASP LYS ASP PRO ASN PHE LYS SEQRES 8 B 108 ASP GLN VAL ILE LEU LEU ASN LYS HIS ILE ASP ALA TYR SEQRES 9 B 108 LYS THR PHE PRO FORMUL 3 HOH *143(H2 O) HELIX 1 AA1 PRO A 258 ARG A 262 5 5 HELIX 2 AA2 ASN A 269 GLY A 275 1 7 HELIX 3 AA3 ASP A 288 GLY A 295 1 8 HELIX 4 AA4 THR A 296 TYR A 298 5 3 HELIX 5 AA5 HIS A 300 GLN A 306 1 7 HELIX 6 AA6 SER A 310 SER A 318 1 9 HELIX 7 AA7 ASN A 345 ILE A 357 1 13 HELIX 8 AA8 ASP A 358 PHE A 363 5 6 HELIX 9 AA9 PRO B 258 ARG B 262 5 5 HELIX 10 AB1 ASN B 269 GLY B 275 1 7 HELIX 11 AB2 ASP B 288 GLY B 295 1 8 HELIX 12 AB3 THR B 296 TYR B 298 5 3 HELIX 13 AB4 HIS B 300 GLN B 306 1 7 HELIX 14 AB5 SER B 310 SER B 318 1 9 HELIX 15 AB6 ASN B 345 ILE B 357 1 13 HELIX 16 AB7 ASP B 358 PHE B 363 5 6 SHEET 1 AA1 4 ARG A 319 THR A 325 0 SHEET 2 AA1 4 GLY A 328 LYS A 338 -1 O TRP A 330 N GLU A 323 SHEET 3 AA1 4 GLY B 328 LYS B 338 -1 O ILE B 337 N LEU A 331 SHEET 4 AA1 4 ARG B 319 THR B 325 -1 N THR B 325 O GLY B 328 CRYST1 103.330 43.490 59.290 90.00 90.00 90.00 P 21 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 0.009678 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022994 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016866 0.00000