HEADER VIRAL PROTEIN 22-JUN-21 7F5F TITLE SARS-COV-2 ORF8 S84 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF8 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 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 GENE: ORF8, ORF8; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, ORF8, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.CHEN,Z.ZHOU,X.CHEN REVDAT 2 29-NOV-23 7F5F 1 REMARK REVDAT 1 19-JAN-22 7F5F 0 JRNL AUTH X.CHEN,Z.ZHOU,C.HUANG,Z.ZHOU,S.KANG,Z.HUANG,G.JIANG,Z.HONG, JRNL AUTH 2 Q.CHEN,M.YANG,S.HE,S.LIU,J.CHEN,K.LI,X.LI,J.LIAO,J.CHEN, JRNL AUTH 3 S.CHEN JRNL TITL CRYSTAL STRUCTURES OF BAT AND HUMAN CORONAVIRUS ORF8 PROTEIN JRNL TITL 2 IG-LIKE DOMAIN PROVIDE INSIGHTS INTO THE DIVERSITY OF IMMUNE JRNL TITL 3 RESPONSES. JRNL REF FRONT IMMUNOL V. 12 07134 2021 JRNL REFN ESSN 1664-3224 JRNL PMID 34975921 JRNL DOI 10.3389/FIMMU.2021.807134 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.369 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 13144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.967 REMARK 3 FREE R VALUE TEST SET COUNT : 1310 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 3.3668 - 2.8000 1.00 1400 151 0.1594 0.1884 REMARK 3 2 3.3668 - 2.6731 1.00 1335 148 0.1786 0.1827 REMARK 3 3 2.6731 - 2.3354 1.00 1317 145 0.1962 0.2290 REMARK 3 4 2.3354 - 2.1220 1.00 1319 146 0.1744 0.2347 REMARK 3 5 2.1220 - 1.9700 1.00 1290 146 0.1791 0.2217 REMARK 3 6 1.9700 - 1.8538 1.00 1292 143 0.1810 0.2215 REMARK 3 7 1.8538 - 1.7610 1.00 1302 143 0.1885 0.2391 REMARK 3 8 1.7610 - 1.6844 1.00 1304 145 0.1819 0.2387 REMARK 3 9 1.6844 - 1.6200 1.00 1275 143 0.1925 0.2149 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.94 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 : 0.006 852 REMARK 3 ANGLE : 0.836 1164 REMARK 3 CHIRALITY : 0.059 126 REMARK 3 PLANARITY : 0.005 151 REMARK 3 DIHEDRAL : 12.669 514 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: NULL REMARK 4 REMARK 4 7F5F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300019876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-20 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13144 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 26.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 58.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 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 1.12_2829 REMARK 200 STARTING MODEL: 7JTL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, CITRIC ACID, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 24.76050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.09550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.34500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.76050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.09550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.34500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.76050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.09550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.34500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.76050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 25.09550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.34500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 CA CA A 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 367 LIES ON A SPECIAL POSITION. 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 53 CG CD CE NZ REMARK 470 ILE A 74 CG1 CG2 CD1 REMARK 470 ILE A 76 CG1 CG2 CD1 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 52 NE CZ NH1 REMARK 480 GLU A 59 CD REMARK 480 ASN A 78 CG REMARK 480 GLU A 106 CD REMARK 480 ASP A 119 CG 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 O HOH A 336 O HOH A 346 2.18 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 78 33.80 -91.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 374 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A 375 DISTANCE = 7.80 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7F8L RELATED DB: PDB DBREF1 7F5F A 18 121 UNP A0A6B9VKN0_SARS2 DBREF2 7F5F A A0A6B9VKN0 18 121 SEQRES 1 A 104 GLN GLU CYS SER LEU GLN SER CYS THR GLN HIS GLN PRO SEQRES 2 A 104 TYR VAL VAL ASP ASP PRO CYS PRO ILE HIS PHE TYR SER SEQRES 3 A 104 LYS TRP TYR ILE ARG VAL GLY ALA ARG LYS SER ALA PRO SEQRES 4 A 104 LEU ILE GLU LEU CYS VAL ASP GLU ALA GLY SER LYS SER SEQRES 5 A 104 PRO ILE GLN TYR ILE ASP ILE GLY ASN TYR THR VAL SER SEQRES 6 A 104 CYS SER PRO PHE THR ILE ASN CYS GLN GLU PRO LYS LEU SEQRES 7 A 104 GLY SER LEU VAL VAL ARG CYS SER PHE TYR GLU ASP PHE SEQRES 8 A 104 LEU GLU TYR HIS ASP VAL ARG VAL VAL LEU ASP PHE ILE HET CA A 201 1 HET CA A 202 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *75(H2 O) SHEET 1 AA1 5 CYS A 20 CYS A 25 0 SHEET 2 AA1 5 ASP A 107 PHE A 120 1 O ARG A 115 N SER A 21 SHEET 3 AA1 5 GLY A 96 PHE A 104 -1 N CYS A 102 O HIS A 112 SHEET 4 AA1 5 PHE A 41 VAL A 49 -1 N TYR A 46 O VAL A 99 SHEET 5 AA1 5 LEU A 57 GLU A 59 -1 O ILE A 58 N ILE A 47 SHEET 1 AA2 3 PRO A 30 VAL A 32 0 SHEET 2 AA2 3 THR A 87 ASN A 89 -1 O ILE A 88 N TYR A 31 SHEET 3 AA2 3 THR A 80 SER A 82 -1 N VAL A 81 O THR A 87 SHEET 1 AA3 2 CYS A 61 GLU A 64 0 SHEET 2 AA3 2 SER A 67 PRO A 70 -1 O SER A 67 N GLU A 64 SSBOND 1 CYS A 20 CYS A 20 1555 2665 2.04 SSBOND 2 CYS A 25 CYS A 90 1555 1555 2.01 SSBOND 3 CYS A 37 CYS A 102 1555 1555 2.03 SSBOND 4 CYS A 61 CYS A 83 1555 1555 2.05 LINK CA CA A 201 O HOH A 369 1555 1555 2.91 CISPEP 1 SER A 84 PRO A 85 0 -1.14 CRYST1 49.521 50.191 80.690 90.00 90.00 90.00 I 2 2 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 0.020193 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012393 0.00000