HEADER UNKNOWN FUNCTION 30-MAY-18 6DKU TITLE CRYSTAL STRUCTURE OF MYOTIS VP35 MUTANT OF INTERFERON INHIBITORY TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VP35; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYOTIS LUCIFUGUS; SOURCE 3 ORGANISM_COMMON: LITTLE BROWN BAT; SOURCE 4 ORGANISM_TAXID: 59463; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR H.LIU,G.M.GINELL,L.J.KEEFE,D.W.LEUNG,G.K.AMARASINGHE REVDAT 4 11-OCT-23 6DKU 1 REMARK REVDAT 3 18-DEC-19 6DKU 1 REMARK REVDAT 2 08-AUG-18 6DKU 1 JRNL REVDAT 1 18-JUL-18 6DKU 0 JRNL AUTH M.R.EDWARDS,H.LIU,R.S.SHABMAN,G.M.GINELL,P.LUTHRA,P.RAMANAN, JRNL AUTH 2 L.J.KEEFE,B.KOLLNER,G.K.AMARASINGHE,D.J.TAYLOR,D.W.LEUNG, JRNL AUTH 3 C.F.BASLER JRNL TITL CONSERVATION OF STRUCTURE AND IMMUNE ANTAGONIST FUNCTIONS OF JRNL TITL 2 FILOVIRAL VP35 HOMOLOGS PRESENT IN MICROBAT GENOMES. JRNL REF CELL REP V. 24 861 2018 JRNL REFN ESSN 2211-1247 JRNL PMID 30044983 JRNL DOI 10.1016/J.CELREP.2018.06.045 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 4662 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.290 REMARK 3 FREE R VALUE TEST SET COUNT : 200 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 39.0674 - 2.6001 0.95 4462 200 0.1711 0.2227 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) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.76 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 : 0.005 1015 REMARK 3 ANGLE : 0.715 1379 REMARK 3 CHIRALITY : 0.049 154 REMARK 3 PLANARITY : 0.005 179 REMARK 3 DIHEDRAL : 10.857 611 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): 4.1838 -30.9361 -5.2976 REMARK 3 T TENSOR REMARK 3 T11: 0.3379 T22: 0.2759 REMARK 3 T33: 0.5509 T12: -0.0023 REMARK 3 T13: -0.0027 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 5.1033 L22: 2.4753 REMARK 3 L33: 7.9976 L12: 0.7509 REMARK 3 L13: 1.8696 L23: 0.9395 REMARK 3 S TENSOR REMARK 3 S11: 0.1849 S12: -0.2503 S13: 0.1916 REMARK 3 S21: 0.1078 S22: -0.0454 S23: 0.2462 REMARK 3 S31: -0.0886 S32: -0.2510 S33: -0.0937 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 6DKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234800. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-16 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 : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.77110 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 OCT 15,2015 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.1.7, XDS OCT 15,2015 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4730 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 39.063 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08730 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.42000 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: MOLREP REMARK 200 STARTING MODEL: 3L25 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 25% (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 28.98067 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 14.49033 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 14.49033 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 28.98067 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 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 GLY A 154 REMARK 465 HIS A 155 REMARK 465 MET A 156 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 ARG A 157 CG CD NE CZ NH1 NH2 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 256 -166.67 -70.24 REMARK 500 PRO A 259 96.29 -60.44 REMARK 500 VAL A 267 -58.70 -122.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 6DKU A 157 270 UNP G9JKD1 G9JKD1_MYOLU 157 270 DBREF 6DKU A 271 281 PDB 6DKU 6DKU 271 281 SEQADV 6DKU GLY A 154 UNP G9JKD1 EXPRESSION TAG SEQADV 6DKU HIS A 155 UNP G9JKD1 EXPRESSION TAG SEQADV 6DKU MET A 156 UNP G9JKD1 EXPRESSION TAG SEQADV 6DKU ASP A 161 UNP G9JKD1 UNK 161 VARIANT SEQADV 6DKU GLY A 171 UNP G9JKD1 SER 171 VARIANT SEQADV 6DKU MET A 189 UNP G9JKD1 UNK 189 VARIANT SEQADV 6DKU MET A 209 UNP G9JKD1 THR 209 VARIANT SEQADV 6DKU GLN A 223 UNP G9JKD1 UNK 223 VARIANT SEQADV 6DKU THR A 236 UNP G9JKD1 UNK 236 VARIANT SEQADV 6DKU ARG A 246 UNP G9JKD1 GLX 246 ENGINEERED MUTATION SEQADV 6DKU TYR A 248 UNP G9JKD1 UNK 248 VARIANT SEQADV 6DKU ARG A 250 UNP G9JKD1 GLY 250 ENGINEERED MUTATION SEQRES 1 A 128 GLY HIS MET ARG LEU PRO LEU ASP PRO THR GLU PHE VAL SEQRES 2 A 128 ARG VAL LEU THR GLY TYR LEU THR GLY PRO ARG THR ALA SEQRES 3 A 128 PHE HIS GLU LEU VAL SER ALA ILE ALA MET VAL SER ARG SEQRES 4 A 128 ASP SER HIS ASP LEU GLN VAL ALA MET ASP HIS PHE ASN SEQRES 5 A 128 ARG GLU LEU MET ASP GLY PHE SER ALA HIS ALA ALA ILE SEQRES 6 A 128 ILE SER ILE THR GLN ARG CYS GLU TYR PHE ARG ASN CYS SEQRES 7 A 128 GLU ALA PRO THR THR GLN VAL THR SER LYS SER GLN ILE SEQRES 8 A 128 PRO ARG ALA TYR HIS ARG ARG LEU ARG ASP VAL PRO GLU SEQRES 9 A 128 GLY PRO LYS THR LEU GLY ARG GLY TRP VAL TYR ILE TYR SEQRES 10 A 128 LEU THR PRO GLU GLY SER LEU GLY LEU LYS ILE FORMUL 2 HOH *7(H2 O) HELIX 1 AA1 ASP A 161 TYR A 172 1 12 HELIX 2 AA2 THR A 178 SER A 191 1 14 HELIX 3 AA3 ASP A 193 ASP A 210 1 18 HELIX 4 AA4 SER A 213 CYS A 225 1 13 HELIX 5 AA5 CYS A 225 ASN A 230 1 6 HELIX 6 AA6 SER A 240 ILE A 244 5 5 HELIX 7 AA7 PRO A 245 LEU A 252 5 8 SHEET 1 AA1 4 THR A 235 GLN A 237 0 SHEET 2 AA1 4 TRP A 266 THR A 272 1 O LEU A 271 N THR A 236 SHEET 3 AA1 4 GLY A 275 LYS A 280 -1 O LEU A 277 N TYR A 270 SHEET 4 AA1 4 ARG A 253 ASP A 254 -1 N ARG A 253 O GLY A 278 CRYST1 78.126 78.126 43.471 90.00 90.00 120.00 P 32 2 1 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 0.012800 0.007390 0.000000 0.00000 SCALE2 0.000000 0.014780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023004 0.00000