HEADER VIRAL PROTEIN 28-MAY-15 5BPV TITLE CRYSTAL STRUCTURE OF ZAIRE EBOLAVIRUS VP35 RNA BINDING DOMAIN MUTANT TITLE 2 I278A COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYMERASE COFACTOR VP35; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RNA BINDING DOMAIN, UNP RESIDUES 217-340; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZAIRE EBOLAVIRUS; SOURCE 3 ORGANISM_COMMON: ZEBOV; SOURCE 4 ORGANISM_TAXID: 186538; SOURCE 5 GENE: VP35; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POLYMERASE COFACTOR, INTERFERON INHIBITOR, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.FADDA,V.CANNAS,L.ZINZULA,S.DISTINTO,G.L.DAINO,G.BIANCO,A.CORONA, AUTHOR 2 F.ESPOSITO,S.ALCARO,E.MACCIONI,E.TRAMONTANO,G.L.TAYLOR REVDAT 2 10-JAN-24 5BPV 1 REMARK REVDAT 1 29-JUN-16 5BPV 0 JRNL AUTH V.FADDA,V.CANNAS,L.ZINZULA,S.DISTINTO,G.L.DAINO,G.BIANCO, JRNL AUTH 2 A.CORONA,F.ESPOSITO,S.ALCARO,E.MACCIONI,E.TRAMONTANO, JRNL AUTH 3 G.L.TAYLOR JRNL TITL CRYSTAL STRUCTURE OF ZAIRE EBOLAVIRUS VP35 RNA BINDING JRNL TITL 2 DOMAIN MUTANT I278A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 939 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 13.9050 - 3.7136 1.00 2636 118 0.1638 0.1836 REMARK 3 2 3.7136 - 2.9569 1.00 2497 146 0.1665 0.2097 REMARK 3 3 2.9569 - 2.5859 1.00 2481 130 0.1846 0.2234 REMARK 3 4 2.5859 - 2.3507 1.00 2474 123 0.1873 0.2290 REMARK 3 5 2.3507 - 2.1829 1.00 2436 149 0.1837 0.2131 REMARK 3 6 2.1829 - 2.0546 1.00 2415 153 0.1939 0.2400 REMARK 3 7 2.0546 - 1.9520 0.99 2456 120 0.2240 0.2854 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) : 23.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.77 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 : 0.007 1993 REMARK 3 ANGLE : 1.030 2710 REMARK 3 CHIRALITY : 0.063 302 REMARK 3 PLANARITY : 0.004 362 REMARK 3 DIHEDRAL : 13.403 764 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5BPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000210172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18397 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.952 REMARK 200 RESOLUTION RANGE LOW (A) : 48.522 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10400 REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : 0.28100 REMARK 200 FOR SHELL : 2.700 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: 3FKE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.87500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.01000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.01000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.87500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.83000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 PRO B 217 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 PRO A 217 CG CD 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 HE21 GLN A 288 O HOH A 403 1.53 REMARK 500 HH22 ARG B 298 O HOH B 404 1.59 REMARK 500 O HOH A 419 O HOH A 479 1.94 REMARK 500 O HOH B 460 O HOH B 524 1.97 REMARK 500 O HOH A 471 O HOH A 507 1.98 REMARK 500 O HOH A 498 O HOH A 517 2.13 REMARK 500 O HOH A 409 O HOH A 490 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 510 O HOH B 523 2464 1.91 REMARK 500 O HOH B 443 O HOH B 485 2465 1.96 REMARK 500 O HOH A 502 O HOH B 526 2464 2.19 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 ARG A 298 -74.15 -88.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 5BPV A 217 340 UNP Q6V1Q9 VP35_EBOZ5 217 340 DBREF 5BPV B 217 340 UNP Q6V1Q9 VP35_EBOZ5 217 340 SEQADV 5BPV ALA A 278 UNP Q6V1Q9 ILE 278 ENGINEERED MUTATION SEQADV 5BPV ALA B 278 UNP Q6V1Q9 ILE 278 ENGINEERED MUTATION SEQRES 1 A 124 PRO ASP ILE SER ALA LYS ASP LEU ARG ASN ILE MET TYR SEQRES 2 A 124 ASP HIS LEU PRO GLY PHE GLY THR ALA PHE HIS GLN LEU SEQRES 3 A 124 VAL GLN VAL ILE CYS LYS LEU GLY LYS ASP SER ASN SER SEQRES 4 A 124 LEU ASP ILE ILE HIS ALA GLU PHE GLN ALA SER LEU ALA SEQRES 5 A 124 GLU GLY ASP SER PRO GLN CYS ALA LEU ALA GLN ILE THR SEQRES 6 A 124 LYS ARG VAL PRO ILE PHE GLN ASP ALA ALA PRO PRO VAL SEQRES 7 A 124 ILE HIS ILE ARG SER ARG GLY ASP ILE PRO ARG ALA CYS SEQRES 8 A 124 GLN LYS SER LEU ARG PRO VAL PRO PRO SER PRO LYS ILE SEQRES 9 A 124 ASP ARG GLY TRP VAL CYS VAL PHE GLN LEU GLN ASP GLY SEQRES 10 A 124 LYS THR LEU GLY LEU LYS ILE SEQRES 1 B 124 PRO ASP ILE SER ALA LYS ASP LEU ARG ASN ILE MET TYR SEQRES 2 B 124 ASP HIS LEU PRO GLY PHE GLY THR ALA PHE HIS GLN LEU SEQRES 3 B 124 VAL GLN VAL ILE CYS LYS LEU GLY LYS ASP SER ASN SER SEQRES 4 B 124 LEU ASP ILE ILE HIS ALA GLU PHE GLN ALA SER LEU ALA SEQRES 5 B 124 GLU GLY ASP SER PRO GLN CYS ALA LEU ALA GLN ILE THR SEQRES 6 B 124 LYS ARG VAL PRO ILE PHE GLN ASP ALA ALA PRO PRO VAL SEQRES 7 B 124 ILE HIS ILE ARG SER ARG GLY ASP ILE PRO ARG ALA CYS SEQRES 8 B 124 GLN LYS SER LEU ARG PRO VAL PRO PRO SER PRO LYS ILE SEQRES 9 B 124 ASP ARG GLY TRP VAL CYS VAL PHE GLN LEU GLN ASP GLY SEQRES 10 B 124 LYS THR LEU GLY LEU LYS ILE FORMUL 3 HOH *263(H2 O) HELIX 1 AA1 SER A 220 LEU A 232 1 13 HELIX 2 AA2 THR A 237 SER A 253 1 17 HELIX 3 AA3 SER A 255 GLU A 269 1 15 HELIX 4 AA4 SER A 272 VAL A 284 1 13 HELIX 5 AA5 PRO A 285 GLN A 288 5 4 HELIX 6 AA6 SER A 299 ILE A 303 5 5 HELIX 7 AA7 PRO A 304 LYS A 309 5 6 HELIX 8 AA8 LYS A 319 ARG A 322 5 4 HELIX 9 AA9 SER B 220 LEU B 232 1 13 HELIX 10 AB1 THR B 237 SER B 253 1 17 HELIX 11 AB2 SER B 255 GLU B 269 1 15 HELIX 12 AB3 SER B 272 VAL B 284 1 13 HELIX 13 AB4 PRO B 285 GLN B 288 5 4 HELIX 14 AB5 SER B 299 ILE B 303 5 5 HELIX 15 AB6 PRO B 304 LYS B 309 5 6 HELIX 16 AB7 LYS B 319 ARG B 322 5 4 SHEET 1 AA1 4 VAL A 294 HIS A 296 0 SHEET 2 AA1 4 TRP A 324 GLN A 329 1 O VAL A 327 N ILE A 295 SHEET 3 AA1 4 THR A 335 LYS A 339 -1 O LEU A 336 N PHE A 328 SHEET 4 AA1 4 LEU A 311 ARG A 312 -1 N ARG A 312 O GLY A 337 SHEET 1 AA2 4 VAL B 294 HIS B 296 0 SHEET 2 AA2 4 TRP B 324 GLN B 329 1 O VAL B 327 N ILE B 295 SHEET 3 AA2 4 THR B 335 LYS B 339 -1 O LEU B 336 N PHE B 328 SHEET 4 AA2 4 LEU B 311 ARG B 312 -1 N ARG B 312 O GLY B 337 CRYST1 51.750 65.660 72.020 90.00 90.00 90.00 P 21 21 21 8 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 0.019324 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013885 0.00000