HEADER VIRAL PROTEIN 22-JAN-25 9MZB TITLE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF ORF9B APO HOMODIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF9B PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ORF9B,ACCESSORY PROTEIN 9B,ORF-9B,PROTEIN 9B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: SARS-COV-2,2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: 9B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: DE3 KEYWDS REFOLDED, APO-HOMODIMER, TYPE-1 INTERFERON SUPPRESSOR, FOLD-SWITCHER, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.J.SAN FELIPE,J.S.FRASER REVDAT 1 26-FEB-25 9MZB 0 JRNL AUTH C.J.SAN FELIPE,J.S.FRASER JRNL TITL X-RAY CRYSTALLOGRAPHIC STRUCTURE OF REFOLDED APO-ORF9B JRNL TITL 2 HOMODIMER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12511 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.291 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.341 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1248 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 37.6400 - 5.8200 1.00 1253 135 0.2471 0.2809 REMARK 3 2 5.8000 - 4.6200 1.00 1272 127 0.2349 0.3118 REMARK 3 3 4.6200 - 4.0400 1.00 1252 143 0.2668 0.3517 REMARK 3 4 4.0300 - 3.6700 1.00 1244 144 0.3244 0.3618 REMARK 3 5 3.6700 - 3.4000 1.00 1242 138 0.3720 0.4246 REMARK 3 6 3.4000 - 3.2000 1.00 1269 147 0.4058 0.4800 REMARK 3 7 3.2000 - 3.0400 1.00 1223 142 0.3570 0.4326 REMARK 3 8 3.0400 - 2.9100 1.00 1282 134 0.3799 0.4411 REMARK 3 9 2.9100 - 2.8000 0.98 1226 138 0.4259 0.4426 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.615 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 50.012 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 97.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 129.5 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 1183 REMARK 3 ANGLE : 0.843 1602 REMARK 3 CHIRALITY : 0.050 210 REMARK 3 PLANARITY : 0.009 197 REMARK 3 DIHEDRAL : 19.242 454 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 22.3149 -29.4025 -14.6730 REMARK 3 T TENSOR REMARK 3 T11: 0.5444 T22: 0.7163 REMARK 3 T33: 0.7716 T12: -0.1262 REMARK 3 T13: -0.1326 T23: -0.1409 REMARK 3 L TENSOR REMARK 3 L11: 9.2176 L22: 7.2403 REMARK 3 L33: 4.4220 L12: -4.4891 REMARK 3 L13: -4.6296 L23: 1.8847 REMARK 3 S TENSOR REMARK 3 S11: -0.2646 S12: -0.1309 S13: 0.5284 REMARK 3 S21: 0.4353 S22: 0.2037 S23: 0.4848 REMARK 3 S31: 0.1670 S32: -0.1401 S33: -0.0363 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 9MZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 193.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.116 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12518 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06155 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 1.18700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.930 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 (%): 59.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M SODIUM PHOSPHATE, 0.8M POTASSIUM REMARK 280 PHOSPHATE, 0.2M LITHIUM SULFATE, AND 0.1M GLYCINE PH 10.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.73667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.47333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.47333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.73667 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: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 PRO A 3 REMARK 465 LYS A 4 REMARK 465 ILE A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 MET A 8 REMARK 465 HIS A 9 REMARK 465 MET A 26 REMARK 465 GLU A 27 REMARK 465 ASN A 28 REMARK 465 ALA A 29 REMARK 465 VAL A 30 REMARK 465 GLY A 31 REMARK 465 ARG A 32 REMARK 465 ASP A 33 REMARK 465 GLN A 34 REMARK 465 ASN A 35 REMARK 465 ASN A 36 REMARK 465 GLY A 49 REMARK 465 SER A 50 REMARK 465 PRO A 51 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 PRO B 3 REMARK 465 LYS B 4 REMARK 465 ILE B 5 REMARK 465 SER B 6 REMARK 465 GLU B 7 REMARK 465 MET B 8 REMARK 465 HIS B 9 REMARK 465 GLN B 34 REMARK 465 ASN B 35 REMARK 465 ARG B 47 REMARK 465 LEU B 48 REMARK 465 GLY B 49 REMARK 465 SER B 50 REMARK 465 PRO B 51 REMARK 465 SER B 63 REMARK 465 LEU B 64 REMARK 465 GLU B 65 REMARK 465 ASP B 66 REMARK 465 LYS B 97 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 LYS A 59 -74.96 -68.85 REMARK 500 THR A 60 -64.53 61.03 REMARK 500 LEU A 61 101.33 -59.11 REMARK 500 ASN A 62 -78.07 -75.50 REMARK 500 SER A 63 172.94 64.65 REMARK 500 ALA A 82 -85.82 -79.70 REMARK 500 ALA B 29 -73.70 -97.80 REMARK 500 THR B 60 -68.84 -120.06 REMARK 500 ALA B 82 -44.93 -138.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 9MZB A 1 97 UNP P0DTD2 ORF9B_SARS2 1 97 DBREF 9MZB B 1 97 UNP P0DTD2 ORF9B_SARS2 1 97 SEQRES 1 A 97 MET ASP PRO LYS ILE SER GLU MET HIS PRO ALA LEU ARG SEQRES 2 A 97 LEU VAL ASP PRO GLN ILE GLN LEU ALA VAL THR ARG MET SEQRES 3 A 97 GLU ASN ALA VAL GLY ARG ASP GLN ASN ASN VAL GLY PRO SEQRES 4 A 97 LYS VAL TYR PRO ILE ILE LEU ARG LEU GLY SER PRO LEU SEQRES 5 A 97 SER LEU ASN MET ALA ARG LYS THR LEU ASN SER LEU GLU SEQRES 6 A 97 ASP LYS ALA PHE GLN LEU THR PRO ILE ALA VAL GLN MET SEQRES 7 A 97 THR LYS LEU ALA THR THR GLU GLU LEU PRO ASP GLU PHE SEQRES 8 A 97 VAL VAL VAL THR VAL LYS SEQRES 1 B 97 MET ASP PRO LYS ILE SER GLU MET HIS PRO ALA LEU ARG SEQRES 2 B 97 LEU VAL ASP PRO GLN ILE GLN LEU ALA VAL THR ARG MET SEQRES 3 B 97 GLU ASN ALA VAL GLY ARG ASP GLN ASN ASN VAL GLY PRO SEQRES 4 B 97 LYS VAL TYR PRO ILE ILE LEU ARG LEU GLY SER PRO LEU SEQRES 5 B 97 SER LEU ASN MET ALA ARG LYS THR LEU ASN SER LEU GLU SEQRES 6 B 97 ASP LYS ALA PHE GLN LEU THR PRO ILE ALA VAL GLN MET SEQRES 7 B 97 THR LYS LEU ALA THR THR GLU GLU LEU PRO ASP GLU PHE SEQRES 8 B 97 VAL VAL VAL THR VAL LYS HET GLY A 101 7 HETNAM GLY GLYCINE FORMUL 3 GLY C2 H5 N O2 FORMUL 4 HOH *(H2 O) HELIX 1 AA1 THR A 83 LEU A 87 5 5 HELIX 2 AA2 ARG B 25 ALA B 29 5 5 HELIX 3 AA3 THR B 83 LEU B 87 5 5 SHEET 1 AA1 6 THR A 79 LYS A 80 0 SHEET 2 AA1 6 ARG A 13 LEU A 14 -1 N LEU A 14 O THR A 79 SHEET 3 AA1 6 ILE A 44 ARG A 47 -1 O LEU A 46 N ARG A 13 SHEET 4 AA1 6 GLU A 90 THR A 95 1 O VAL A 94 N ARG A 47 SHEET 5 AA1 6 SER B 53 LYS B 59 -1 O ALA B 57 N PHE A 91 SHEET 6 AA1 6 PHE B 69 PRO B 73 -1 O THR B 72 N MET B 56 SHEET 1 AA2 4 LYS A 40 TYR A 42 0 SHEET 2 AA2 4 ILE A 19 VAL A 23 -1 N VAL A 23 O LYS A 40 SHEET 3 AA2 4 ILE B 19 VAL B 23 -1 O ALA B 22 N GLN A 20 SHEET 4 AA2 4 LYS B 40 TYR B 42 -1 O TYR B 42 N LEU B 21 SHEET 1 AA3 6 GLN A 70 PRO A 73 0 SHEET 2 AA3 6 SER A 53 ARG A 58 -1 N ARG A 58 O GLN A 70 SHEET 3 AA3 6 GLU B 90 THR B 95 -1 O VAL B 93 N ASN A 55 SHEET 4 AA3 6 ILE B 44 LEU B 46 1 N ILE B 45 O VAL B 92 SHEET 5 AA3 6 ARG B 13 VAL B 15 -1 N VAL B 15 O ILE B 44 SHEET 6 AA3 6 MET B 78 LYS B 80 -1 O THR B 79 N LEU B 14 CRYST1 75.280 75.280 80.210 90.00 90.00 120.00 P 31 2 1 12 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 0.013284 0.007669 0.000000 0.00000 SCALE2 0.000000 0.015339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012467 0.00000 MASTER 301 0 1 3 16 0 0 6 1174 2 0 16 END