HEADER VIRAL PROTEIN 16-AUG-22 7YTT TITLE CRYSTAL STRUCTURE OF VACCINIA VIRUS G3/L5 SUB-COMPLEX (SEMET-LABELED, TITLE 2 P21 SPACE GROUP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN G3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN L5; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: PROTEIN F6; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS (STRAIN WESTERN RESERVE); SOURCE 3 ORGANISM_COMMON: VACV, VACCINIA VIRUS (STRAIN WR); SOURCE 4 ORGANISM_TAXID: 10254; SOURCE 5 STRAIN: WESTERN RESERVE; SOURCE 6 GENE: VACWR079, G3L; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: VACCINIA VIRUS (STRAIN WESTERN RESERVE); SOURCE 11 ORGANISM_COMMON: VACV, VACCINIA VIRUS (STRAIN WR); SOURCE 12 ORGANISM_TAXID: 10254; SOURCE 13 STRAIN: WESTERN RESERVE; SOURCE 14 GENE: VACWR092, L5R; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS THE COMPONENTS OF ENTRY-FUSION COMPLEX, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LIN,D.YUE,G.W.LU REVDAT 1 08-FEB-23 7YTT 0 JRNL AUTH S.LIN,D.YUE,F.YANG,Z.CHEN,B.HE,Y.CAO,H.DONG,J.LI,Q.ZHAO,G.LU JRNL TITL CRYSTAL STRUCTURE OF VACCINIA VIRUS G3/L5 SUB-COMPLEX JRNL TITL 2 REVEALS A NOVEL FOLD WITH EXTENDED INTER-MOLECULE JRNL TITL 3 INTERACTIONS CONSERVED AMONG ORTHOPOXVIRUSES. JRNL REF EMERG MICROBES INFECT V. 12 60661 2023 JRNL REFN ESSN 2222-1751 JRNL PMID 36533407 JRNL DOI 10.1080/22221751.2022.2160661 REMARK 2 REMARK 2 RESOLUTION. 1.81 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 11674 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 592 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 29.2480 - 2.8726 0.99 2827 171 0.1798 0.1877 REMARK 3 2 2.8726 - 2.2803 1.00 2797 163 0.2263 0.2323 REMARK 3 3 2.2803 - 1.9921 1.00 2810 126 0.2144 0.2556 REMARK 3 4 1.9921 - 1.8100 0.94 2648 132 0.2185 0.2842 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) : 27.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.91 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 : 0.004 1136 REMARK 3 ANGLE : 0.744 1539 REMARK 3 CHIRALITY : 0.052 185 REMARK 3 PLANARITY : 0.004 194 REMARK 3 DIHEDRAL : 14.078 714 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): 4.3902 1.6321 16.1136 REMARK 3 T TENSOR REMARK 3 T11: 0.1602 T22: 0.1875 REMARK 3 T33: 0.1800 T12: -0.0090 REMARK 3 T13: -0.0196 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 3.2647 L22: 2.7012 REMARK 3 L33: 2.8460 L12: -0.3423 REMARK 3 L13: -0.1465 L23: 0.4115 REMARK 3 S TENSOR REMARK 3 S11: -0.0444 S12: 0.0908 S13: 0.1282 REMARK 3 S21: -0.0462 S22: -0.0390 S23: 0.0106 REMARK 3 S31: -0.1216 S32: -0.0720 S33: 0.0264 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 7YTT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 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) : 0.97892 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.54400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM NITRATE (PH 6.2), 20% REMARK 280 W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 20.95950 REMARK 290 SMTRY3 2 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: 3190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 20 REMARK 465 PRO A 21 REMARK 465 TYR A 22 REMARK 465 TYR A 23 REMARK 465 PRO A 24 REMARK 465 THR A 25 REMARK 465 ASN A 26 REMARK 465 LYS A 27 REMARK 465 LEU A 28 REMARK 465 GLN A 29 REMARK 465 ALA A 30 REMARK 465 ALA A 31 REMARK 465 VAL A 32 REMARK 465 MSE A 33 REMARK 465 GLU A 34 REMARK 465 THR A 35 REMARK 465 ASP A 36 REMARK 465 ARG A 37 REMARK 465 GLU A 38 REMARK 465 ASN A 39 REMARK 465 GLY B 50 REMARK 465 PRO B 51 REMARK 465 ASN B 52 REMARK 465 MSE B 53 REMARK 465 PHE B 54 REMARK 465 PHE B 55 REMARK 465 MSE B 56 REMARK 465 PRO B 57 REMARK 465 LYS B 58 REMARK 465 ARG B 59 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 B 227 O HOH B 230 2.14 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 ASP B 77 -119.26 49.57 REMARK 500 SER B 99 37.29 70.66 REMARK 500 ASP B 106 36.65 -93.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 7YTT A 22 111 UNP P68458 G3_VACCW 22 111 DBREF 7YTT B 52 128 UNP P68623 L5_VACCW 52 128 SEQADV 7YTT GLY A 20 UNP P68458 EXPRESSION TAG SEQADV 7YTT PRO A 21 UNP P68458 EXPRESSION TAG SEQADV 7YTT GLY B 50 UNP P68623 EXPRESSION TAG SEQADV 7YTT PRO B 51 UNP P68623 EXPRESSION TAG SEQRES 1 A 92 GLY PRO TYR TYR PRO THR ASN LYS LEU GLN ALA ALA VAL SEQRES 2 A 92 MSE GLU THR ASP ARG GLU ASN ALA ILE ILE ARG GLN ARG SEQRES 3 A 92 ASN ASP GLU ILE PRO THR ARG THR LEU ASP THR ALA ILE SEQRES 4 A 92 PHE THR ASP ALA SER THR VAL ALA SER ALA GLN ILE HIS SEQRES 5 A 92 LEU TYR TYR ASN SER ASN ILE GLY LYS ILE ILE MSE SER SEQRES 6 A 92 LEU ASN GLY LYS LYS HIS THR PHE ASN LEU TYR ASP ASP SEQRES 7 A 92 ASN ASP ILE ARG THR LEU LEU PRO ILE LEU LEU LEU SER SEQRES 8 A 92 LYS SEQRES 1 B 79 GLY PRO ASN MSE PHE PHE MSE PRO LYS ARG LYS ILE PRO SEQRES 2 B 79 ASP PRO ILE ASP ARG LEU ARG ARG ALA ASN LEU ALA CYS SEQRES 3 B 79 GLU ASP ASP LYS LEU MSE ILE TYR GLY LEU PRO TRP MSE SEQRES 4 B 79 THR THR GLN THR SER ALA LEU SER ILE ASN SER LYS PRO SEQRES 5 B 79 ILE VAL TYR LYS ASP CYS ALA LYS LEU LEU ARG SER ILE SEQRES 6 B 79 ASN GLY SER GLN PRO VAL SER LEU ASN ASP VAL LEU ARG SEQRES 7 B 79 ARG MODRES 7YTT MSE A 83 MET MODIFIED RESIDUE MODRES 7YTT MSE B 81 MET MODIFIED RESIDUE MODRES 7YTT MSE B 88 MET MODIFIED RESIDUE HET MSE A 83 8 HET MSE B 81 8 HET MSE B 88 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 3 HOH *62(H2 O) HELIX 1 AA1 ILE A 41 ASP A 47 1 7 HELIX 2 AA2 ASP A 96 LEU A 109 1 14 HELIX 3 AA3 ILE B 65 ARG B 69 5 5 HELIX 4 AA4 ASP B 106 GLY B 116 1 11 HELIX 5 AA5 SER B 121 ARG B 127 1 7 SHEET 1 AA1 4 LEU A 54 ASP A 61 0 SHEET 2 AA1 4 THR A 64 ASN A 75 -1 O ALA A 68 N THR A 56 SHEET 3 AA1 4 LYS A 80 LEU A 85 -1 O SER A 84 N HIS A 71 SHEET 4 AA1 4 LYS A 88 ASN A 93 -1 O HIS A 90 N MSE A 83 SHEET 1 AA2 3 ASN B 72 GLU B 76 0 SHEET 2 AA2 3 LYS B 79 TYR B 83 -1 O TYR B 83 N ASN B 72 SHEET 3 AA2 3 THR B 92 SER B 93 -1 O THR B 92 N ILE B 82 SSBOND 1 CYS B 75 CYS B 107 1555 1555 2.04 LINK C ILE A 82 N MSE A 83 1555 1555 1.33 LINK C MSE A 83 N SER A 84 1555 1555 1.33 LINK C LEU B 80 N MSE B 81 1555 1555 1.33 LINK C MSE B 81 N ILE B 82 1555 1555 1.33 LINK C TRP B 87 N MSE B 88 1555 1555 1.33 LINK C MSE B 88 N THR B 89 1555 1555 1.33 CISPEP 1 ALA A 40 ILE A 41 0 11.09 CRYST1 29.277 41.919 53.184 90.00 92.54 90.00 P 1 21 1 2 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 0.034157 0.000000 0.001518 0.00000 SCALE2 0.000000 0.023856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018821 0.00000