HEADER ANTIVIRAL PROTEIN 12-JAN-19 6J62 TITLE CRYSTAL STRUCTURE OF MISG15/NS1B COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE PROTEIN ISG15; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INTERFERON-INDUCED 15 KDA PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NON-STRUCTURAL PROTEIN 1; COMPND 8 CHAIN: C; COMPND 9 SYNONYM: NS1,NS1A; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ISG15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: INFLUENZA B VIRUS (STRAIN B/LEE/1940); SOURCE 11 ORGANISM_TAXID: 518987; SOURCE 12 STRAIN: B/LEE/1940; SOURCE 13 GENE: NS; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS COMPLEX, ANTIVIRAL, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.N.JIANG,X.Q.WANG REVDAT 2 27-MAR-24 6J62 1 REMARK REVDAT 1 25-DEC-19 6J62 0 JRNL AUTH Y.N.JIANG,X.Q.WANG JRNL TITL CRYSTAL STRUCTURE OF MISG15/NS1B COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 10201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 485 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 38.9841 - 3.5844 0.99 3330 165 0.1730 0.2371 REMARK 3 2 3.5844 - 2.8453 1.00 3269 157 0.2713 0.3765 REMARK 3 3 2.8453 - 2.4857 0.96 3117 163 0.2917 0.3840 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1957 REMARK 3 ANGLE : 0.972 2631 REMARK 3 CHIRALITY : 0.048 294 REMARK 3 PLANARITY : 0.005 338 REMARK 3 DIHEDRAL : 16.505 1204 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 2:78 REMARK 3 ORIGIN FOR THE GROUP (A): 110.1834 -8.1959 22.4572 REMARK 3 T TENSOR REMARK 3 T11: 0.5812 T22: 0.7605 REMARK 3 T33: 0.5141 T12: 0.1180 REMARK 3 T13: 0.0668 T23: -0.1043 REMARK 3 L TENSOR REMARK 3 L11: 7.2152 L22: 6.9194 REMARK 3 L33: 4.6782 L12: -2.3977 REMARK 3 L13: 0.1940 L23: -3.2289 REMARK 3 S TENSOR REMARK 3 S11: -0.4384 S12: -0.7101 S13: 0.1516 REMARK 3 S21: 0.1754 S22: 0.2260 S23: -0.1722 REMARK 3 S31: -0.1469 S32: -0.1495 S33: 0.1683 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 79:151 REMARK 3 ORIGIN FOR THE GROUP (A): 82.4190 -1.3794 25.9509 REMARK 3 T TENSOR REMARK 3 T11: 0.5439 T22: 0.8851 REMARK 3 T33: 0.8570 T12: 0.0957 REMARK 3 T13: 0.0426 T23: 0.1194 REMARK 3 L TENSOR REMARK 3 L11: 9.0034 L22: 5.9761 REMARK 3 L33: 9.7026 L12: -3.4228 REMARK 3 L13: -2.6171 L23: 0.6561 REMARK 3 S TENSOR REMARK 3 S11: -0.3044 S12: -0.1905 S13: -1.0830 REMARK 3 S21: 0.1128 S22: 0.2876 S23: 0.8976 REMARK 3 S31: 0.3855 S32: -0.8611 S33: -0.0041 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 100.2777 7.2188 -1.5788 REMARK 3 T TENSOR REMARK 3 T11: 0.5780 T22: 0.5752 REMARK 3 T33: 0.5895 T12: -0.0343 REMARK 3 T13: -0.0008 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 2.8321 L22: 4.2994 REMARK 3 L33: 3.1260 L12: -0.1161 REMARK 3 L13: 0.8757 L23: -0.1775 REMARK 3 S TENSOR REMARK 3 S11: -0.1281 S12: 0.2045 S13: -0.1930 REMARK 3 S21: -0.2501 S22: 0.2926 S23: 0.3038 REMARK 3 S31: 0.0555 S32: -0.1966 S33: -2.1244 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 6J62 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-18 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 : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10221 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 35.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MAGNESIUM CHLORIDE, 0.1M NA REMARK 280 -HEPES, PH 7.0, 13 %(W/V) PEG 4000., VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 54.05650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.88300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.05650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.88300 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 APPLY THE FOLLOWING TO CHAINS: 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 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 LEU A 152 REMARK 465 ARG A 153 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 ASP C 3 REMARK 465 ASN C 4 REMARK 465 MET C 5 REMARK 465 THR C 6 REMARK 465 THR C 7 REMARK 465 THR C 8 REMARK 465 GLU C 101 REMARK 465 PRO C 102 REMARK 465 TYR C 103 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 PRO A 39 133.22 -36.98 REMARK 500 THR A 49 -6.04 68.13 REMARK 500 ASN A 75 -158.58 -99.38 REMARK 500 CYS A 76 137.65 -171.24 REMARK 500 SER C 65 20.86 -75.66 REMARK 500 MET C 91 73.52 41.51 REMARK 500 ASP C 92 119.62 -163.34 REMARK 500 GLU C 98 -29.06 178.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 6J62 A 1 153 UNP Q64339 ISG15_MOUSE 1 153 DBREF 6J62 C 1 103 UNP P03502 NS1_INBLE 1 103 SEQRES 1 A 153 MET ALA TRP ASP LEU LYS VAL LYS MET LEU GLY GLY ASN SEQRES 2 A 153 ASP PHE LEU VAL SER VAL THR ASN SER MET THR VAL SER SEQRES 3 A 153 GLU LEU LYS LYS GLN ILE ALA GLN LYS ILE GLY VAL PRO SEQRES 4 A 153 ALA PHE GLN GLN ARG LEU ALA HIS GLN THR ALA VAL LEU SEQRES 5 A 153 GLN ASP GLY LEU THR LEU SER SER LEU GLY LEU GLY PRO SEQRES 6 A 153 SER SER THR VAL MET LEU VAL VAL GLN ASN CYS SER GLU SEQRES 7 A 153 PRO LEU SER ILE LEU VAL ARG ASN GLU ARG GLY HIS SER SEQRES 8 A 153 ASN ILE TYR GLU VAL PHE LEU THR GLN THR VAL ASP THR SEQRES 9 A 153 LEU LYS LYS LYS VAL SER GLN ARG GLU GLN VAL HIS GLU SEQRES 10 A 153 ASP GLN PHE TRP LEU SER PHE GLU GLY ARG PRO MET GLU SEQRES 11 A 153 ASP LYS GLU LEU LEU GLY GLU TYR GLY LEU LYS PRO GLN SEQRES 12 A 153 CYS THR VAL ILE LYS HIS LEU ARG LEU ARG SEQRES 1 C 103 MET ALA ASP ASN MET THR THR THR GLN ILE GLU VAL GLY SEQRES 2 C 103 PRO GLY ALA THR ASN ALA THR ILE ASN PHE GLU ALA GLY SEQRES 3 C 103 ILE LEU GLU CYS TYR GLU ARG PHE SER TRP GLN ARG ALA SEQRES 4 C 103 LEU ASP TYR PRO GLY GLN ASP ARG LEU HIS ARG LEU LYS SEQRES 5 C 103 ARG LYS LEU GLU SER ARG ILE LYS THR HIS ASN LYS SER SEQRES 6 C 103 GLU PRO GLU ASN LYS ARG MET SER LEU GLU GLU ARG LYS SEQRES 7 C 103 ALA ILE GLY VAL LYS MET MET LYS VAL LEU LEU PHE MET SEQRES 8 C 103 ASP PRO SER ALA GLY ILE GLU GLY PHE GLU PRO TYR HELIX 1 AA1 THR A 24 GLY A 37 1 14 HELIX 2 AA2 PRO A 39 PHE A 41 5 3 HELIX 3 AA3 THR A 101 GLN A 114 1 14 HELIX 4 AA4 HIS A 116 ASP A 118 5 3 HELIX 5 AA5 LEU A 134 GLY A 139 5 6 HELIX 6 AA6 GLY C 15 GLN C 37 1 23 HELIX 7 AA7 ASP C 41 ASN C 63 1 23 HELIX 8 AA8 PRO C 67 ARG C 71 5 5 HELIX 9 AA9 SER C 73 MET C 91 1 19 SHEET 1 AA1 5 ASP A 14 VAL A 19 0 SHEET 2 AA1 5 TRP A 3 MET A 9 -1 N TRP A 3 O VAL A 19 SHEET 3 AA1 5 THR A 68 VAL A 73 1 O VAL A 69 N LYS A 6 SHEET 4 AA1 5 GLN A 43 HIS A 47 -1 N ALA A 46 O MET A 70 SHEET 5 AA1 5 ALA A 50 VAL A 51 -1 O ALA A 50 N HIS A 47 SHEET 1 AA2 5 SER A 91 VAL A 96 0 SHEET 2 AA2 5 LEU A 80 ARG A 85 -1 N ILE A 82 O TYR A 94 SHEET 3 AA2 5 THR A 145 LEU A 150 1 O VAL A 146 N LEU A 83 SHEET 4 AA2 5 PHE A 120 PHE A 124 -1 N TRP A 121 O HIS A 149 SHEET 5 AA2 5 ARG A 127 MET A 129 -1 O ARG A 127 N PHE A 124 CRYST1 108.113 37.766 72.531 90.00 101.35 90.00 C 1 2 1 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 0.009250 0.000000 0.001856 0.00000 SCALE2 0.000000 0.026479 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014062 0.00000