HEADER VIRAL PROTEIN 01-JUL-19 6S5I TITLE STRUCTURE OF THE LAUSANNE VARIANT OF MYXOMA VIRUS M062 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: M62R; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYXOMA VIRUS; SOURCE 3 ORGANISM_TAXID: 10273; SOURCE 4 GENE: M062R, M062R, MYXV_GP066; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI STR. 'CLONE D I2'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 885276 KEYWDS MYXOMA VIRUS, M062, SAMD9, C7L SUPERFAMILY, HOST-RANGE FACTOR, INNATE KEYWDS 2 IMMUNITY, VIRAL ANTAGONISM, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.O'BYRNE,A.R.KHAN REVDAT 2 24-JAN-24 6S5I 1 REMARK REVDAT 1 01-DEC-21 6S5I 0 JRNL AUTH P.O'BYRNE,A.R.KHAN JRNL TITL STRUCTURE OF THE LAUSANNE VARIANT OF MYXOMA VIRUS M062 JRNL TITL 2 PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.290 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8469 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.310 REMARK 3 FREE R VALUE TEST SET COUNT : 873 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 0.0000 - 4.4500 0.98 1290 144 0.1771 0.2038 REMARK 3 2 4.4500 - 3.5300 1.00 1276 151 0.1984 0.2658 REMARK 3 3 3.5300 - 3.0900 1.00 1267 138 0.2362 0.3351 REMARK 3 4 3.0900 - 2.8000 1.00 1242 160 0.2620 0.3621 REMARK 3 5 2.8000 - 2.6000 1.00 1242 154 0.3430 0.4101 REMARK 3 6 2.6000 - 2.4500 1.00 1279 126 0.4620 0.4875 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) : 0.352 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 84.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 96.52 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 : 0.014 1295 REMARK 3 ANGLE : 1.803 1748 REMARK 3 CHIRALITY : 0.109 197 REMARK 3 PLANARITY : 0.008 215 REMARK 3 DIHEDRAL : 16.052 484 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): 8.5101 34.1145 34.3344 REMARK 3 T TENSOR REMARK 3 T11: 0.6544 T22: 0.8433 REMARK 3 T33: 0.6976 T12: 0.0031 REMARK 3 T13: 0.0806 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 4.4085 L22: 3.8595 REMARK 3 L33: 3.6844 L12: -0.0517 REMARK 3 L13: 2.4249 L23: 1.4463 REMARK 3 S TENSOR REMARK 3 S11: 0.1364 S12: 0.1045 S13: -0.2541 REMARK 3 S21: 0.0466 S22: -0.3291 S23: 0.2793 REMARK 3 S31: 0.1278 S32: -0.4667 S33: -0.0001 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 6S5I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292101969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8422 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 47.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.05385 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: 3CZ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 7.5 50 MM CACL2 6 - 8% REMARK 280 PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 14.71200 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 29.42400 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.71200 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 29.42400 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: 80 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 PHE A 145 REMARK 465 VAL A 146 REMARK 465 GLU A 147 REMARK 465 HIS A 157 REMARK 465 SER A 158 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 LEU A 23 131.35 -36.24 REMARK 500 CYS A 31 132.34 -170.16 REMARK 500 ASP A 55 65.01 -119.04 REMARK 500 GLU A 56 79.35 -176.97 REMARK 500 MET A 128 51.08 -99.47 REMARK 500 TYR A 130 56.06 -103.71 REMARK 500 ASN A 149 40.91 -176.72 REMARK 500 TRP A 151 151.89 86.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A -2 N REMARK 620 2 SER A -1 N 81.2 REMARK 620 3 HIS A 0 N 161.2 81.7 REMARK 620 4 HIS A 0 ND1 109.7 162.3 85.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 201 DBREF 6S5I A 1 158 UNP B2CWG9 B2CWG9_9POXV 1 158 SEQADV 6S5I GLY A -2 UNP B2CWG9 EXPRESSION TAG SEQADV 6S5I SER A -1 UNP B2CWG9 EXPRESSION TAG SEQADV 6S5I HIS A 0 UNP B2CWG9 EXPRESSION TAG SEQADV 6S5I SER A 90 UNP B2CWG9 CYS 90 ENGINEERED MUTATION SEQADV 6S5I SER A 107 UNP B2CWG9 CYS 107 ENGINEERED MUTATION SEQADV 6S5I SER A 143 UNP B2CWG9 CYS 143 ENGINEERED MUTATION SEQRES 1 A 161 GLY SER HIS MET GLY VAL GLN HIS LYS LEU ASP ILE PHE SEQRES 2 A 161 LEU VAL SER GLU GLY ILE ALA ILE LYS GLU ALA ASN LEU SEQRES 3 A 161 LEU LYS GLY ASP SER TYR GLY CYS THR ILE LYS ILE LYS SEQRES 4 A 161 LEU ASP LYS GLU LYS THR PHE LYS PHE VAL ILE VAL LEU SEQRES 5 A 161 GLU PRO GLU TRP ILE ASP GLU ILE LYS PRO ILE TYR MET SEQRES 6 A 161 LYS VAL ASN ASP GLU SER VAL GLU LEU GLU LEU ASP TYR SEQRES 7 A 161 LYS ASP ALA ILE LYS ARG ILE TYR SER ALA GLU VAL VAL SEQRES 8 A 161 LEU SER SER ASP SER VAL ILE ASN LEU PHE SER ASP VAL SEQRES 9 A 161 ASP VAL SER TYR THR SER GLU TYR PRO THR ILE LYS VAL SEQRES 10 A 161 ASN THR ILE LYS LYS TYR TYR SER VAL GLN ASN ARG GLY SEQRES 11 A 161 MET THR TYR VAL HIS ILE GLU SER PRO ILE ASN THR LYS SEQRES 12 A 161 ASP LYS SER TRP PHE VAL GLU LYS ASN GLY TRP TYR GLU SEQRES 13 A 161 ASP ARG THR HIS SER HET NI A 201 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ HELIX 1 AA1 ASP A 102 SER A 107 1 6 HELIX 2 AA2 ASN A 138 LYS A 142 5 5 SHEET 1 AA1 6 GLU A 72 LYS A 76 0 SHEET 2 AA1 6 ARG A 81 LEU A 89 -1 O SER A 84 N GLU A 72 SHEET 3 AA1 6 LYS A 41 GLU A 50 -1 N PHE A 45 O ALA A 85 SHEET 4 AA1 6 LYS A 6 LEU A 11 -1 N LYS A 6 O GLU A 50 SHEET 5 AA1 6 ILE A 16 LYS A 19 -1 O ILE A 18 N ILE A 9 SHEET 6 AA1 6 HIS A 132 GLU A 134 -1 O GLU A 134 N ALA A 17 SHEET 1 AA2 6 GLU A 67 VAL A 69 0 SHEET 2 AA2 6 TYR A 61 VAL A 64 -1 N VAL A 64 O GLU A 67 SHEET 3 AA2 6 SER A 93 PHE A 98 -1 O PHE A 98 N TYR A 61 SHEET 4 AA2 6 GLY A 30 LYS A 36 -1 N ILE A 33 O ILE A 95 SHEET 5 AA2 6 THR A 111 ASN A 115 1 O ILE A 112 N LYS A 34 SHEET 6 AA2 6 TYR A 120 ASN A 125 -1 O TYR A 120 N ASN A 115 LINK N GLY A -2 NI NI A 201 1555 1555 2.36 LINK N SER A -1 NI NI A 201 1555 1555 2.07 LINK N HIS A 0 NI NI A 201 1555 1555 2.19 LINK ND1 HIS A 0 NI NI A 201 1555 1555 2.17 CISPEP 1 SER A 135 PRO A 136 0 0.22 SITE 1 AC1 4 GLY A -2 SER A -1 HIS A 0 MET A 1 CRYST1 94.827 94.827 44.136 90.00 90.00 120.00 P 64 6 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 0.010546 0.006088 0.000000 0.00000 SCALE2 0.000000 0.012177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022657 0.00000