HEADER VIRAL PROTEIN 07-APR-00 1ES6 TITLE CRYSTAL STRUCTURE OF THE MATRIX PROTEIN OF EBOLA VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX PROTEIN VP40; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EBOLA VIRUS SP.; SOURCE 3 ORGANISM_TAXID: 205488; SOURCE 4 STRAIN: ZAIRE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PRSET; SOURCE 8 OTHER_DETAILS: EBOLA VIRUS RNA GENOME KEYWDS BETA SANDWICH, ANTI-PARALLEL STRANDS, BETA SHEET, HELIX, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.DESSEN,V.VOLCHKOV,O.DOLNIK,H.-D.KLENK,W.WEISSENHORN REVDAT 5 07-FEB-24 1ES6 1 REMARK REVDAT 4 03-NOV-21 1ES6 1 SEQADV REVDAT 3 24-FEB-09 1ES6 1 VERSN REVDAT 2 01-APR-03 1ES6 1 JRNL REVDAT 1 30-AUG-00 1ES6 0 JRNL AUTH A.DESSEN,V.VOLCHKOV,O.DOLNIK,H.D.KLENK,W.WEISSENHORN JRNL TITL CRYSTAL STRUCTURE OF THE MATRIX PROTEIN VP40 FROM EBOLA JRNL TITL 2 VIRUS. JRNL REF EMBO J. V. 19 4228 2000 JRNL REFN ISSN 0261-4189 JRNL PMID 10944105 JRNL DOI 10.1093/EMBOJ/19.16.4228 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.DESSEN,E.FOREST,V.VOLCHKOV,O.DOLNIK,H.-D.KLENK, REMARK 1 AUTH 2 W.WEISSENHORN REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF THE MATRIX REMARK 1 TITL 2 PROTEIN FROM EBOLA VIRUS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 758 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444900004388 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 17007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1857 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1965 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.59 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.470 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ES6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010849. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8855 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17806 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.22400 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: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, PEG 750 MONOMETHYLETHER, REMARK 280 MAGNESIUM CHLORIDE, BETA-OCTYLGLUCOSIDE , PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 32.31850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.54700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.31850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.54700 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: 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 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 ASN A 31 REMARK 465 SER A 32 REMARK 465 ASN A 33 REMARK 465 THR A 34 REMARK 465 GLY A 35 REMARK 465 PHE A 36 REMARK 465 LEU A 37 REMARK 465 THR A 38 REMARK 465 PRO A 39 REMARK 465 GLU A 40 REMARK 465 SER A 41 REMARK 465 VAL A 42 REMARK 465 ASN A 43 REMARK 465 THR A 195 REMARK 465 PRO A 196 REMARK 465 THR A 197 REMARK 465 GLY A 198 REMARK 465 SER A 199 REMARK 465 ASN A 200 REMARK 465 SER A 222 REMARK 465 GLY A 223 REMARK 465 LYS A 224 REMARK 465 LYS A 225 REMARK 465 GLY A 226 REMARK 465 LYS A 274 REMARK 465 LYS A 275 REMARK 465 VAL A 276 REMARK 465 THR A 277 REMARK 465 SER A 278 REMARK 465 LYS A 279 REMARK 465 ASN A 280 REMARK 465 ALA A 322 REMARK 465 VAL A 323 REMARK 465 ILE A 324 REMARK 465 GLU A 325 REMARK 465 LYS A 326 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 LYS A 221 CG CD CE NZ REMARK 470 ASN A 227 CG OD1 ND2 REMARK 470 SER A 228 OG REMARK 470 ASP A 230 CG OD1 OD2 REMARK 470 GLN A 238 CG CD OE1 NE2 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 A 45 -149.95 -161.96 REMARK 500 LEU A 117 34.55 -95.90 REMARK 500 ALA A 202 107.53 60.97 REMARK 500 ILE A 252 -53.06 -127.67 REMARK 500 TYR A 292 55.07 -105.27 REMARK 500 LEU A 295 -144.81 37.40 REMARK 500 ASP A 296 126.94 177.53 REMARK 500 VAL A 298 -23.95 -25.57 REMARK 500 ASP A 302 121.29 67.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 1ES6 A 31 326 UNP Q913A4 Q913A4_9MONO 31 326 SEQADV 1ES6 LEU A 269 UNP Q913A4 HIS 269 ENGINEERED MUTATION SEQRES 1 A 296 ASN SER ASN THR GLY PHE LEU THR PRO GLU SER VAL ASN SEQRES 2 A 296 GLY ASP THR PRO SER ASN PRO LEU ARG PRO ILE ALA ASP SEQRES 3 A 296 ASP THR ILE ASP HIS ALA SER HIS THR PRO GLY SER VAL SEQRES 4 A 296 SER SER ALA PHE ILE LEU GLU ALA MET VAL ASN VAL ILE SEQRES 5 A 296 SER GLY PRO LYS VAL LEU MET LYS GLN ILE PRO ILE TRP SEQRES 6 A 296 LEU PRO LEU GLY VAL ALA ASP GLN LYS THR TYR SER PHE SEQRES 7 A 296 ASP SER THR THR ALA ALA ILE MET LEU ALA SER TYR THR SEQRES 8 A 296 ILE THR HIS PHE GLY LYS ALA THR ASN PRO LEU VAL ARG SEQRES 9 A 296 VAL ASN ARG LEU GLY PRO GLY ILE PRO ASP HIS PRO LEU SEQRES 10 A 296 ARG LEU LEU ARG ILE GLY ASN GLN ALA PHE LEU GLN GLU SEQRES 11 A 296 PHE VAL LEU PRO PRO VAL GLN LEU PRO GLN TYR PHE THR SEQRES 12 A 296 PHE ASP LEU THR ALA LEU LYS LEU ILE THR GLN PRO LEU SEQRES 13 A 296 PRO ALA ALA THR TRP THR ASP ASP THR PRO THR GLY SER SEQRES 14 A 296 ASN GLY ALA LEU ARG PRO GLY ILE SER PHE HIS PRO LYS SEQRES 15 A 296 LEU ARG PRO ILE LEU LEU PRO ASN LYS SER GLY LYS LYS SEQRES 16 A 296 GLY ASN SER ALA ASP LEU THR SER PRO GLU LYS ILE GLN SEQRES 17 A 296 ALA ILE MET THR SER LEU GLN ASP PHE LYS ILE VAL PRO SEQRES 18 A 296 ILE ASP PRO THR LYS ASN ILE MET GLY ILE GLU VAL PRO SEQRES 19 A 296 GLU THR LEU VAL LEU LYS LEU THR GLY LYS LYS VAL THR SEQRES 20 A 296 SER LYS ASN GLY GLN PRO ILE ILE PRO VAL LEU LEU PRO SEQRES 21 A 296 LYS TYR ILE GLY LEU ASP PRO VAL ALA PRO GLY ASP LEU SEQRES 22 A 296 THR MET VAL ILE THR GLN ASP CYS ASP THR CYS HIS SER SEQRES 23 A 296 PRO ALA SER LEU PRO ALA VAL ILE GLU LYS FORMUL 2 HOH *120(H2 O) HELIX 1 1 ASP A 60 HIS A 64 5 5 HELIX 2 2 SER A 107 LEU A 117 1 11 HELIX 3 3 LEU A 147 GLY A 153 1 7 HELIX 4 4 GLN A 159 LEU A 163 1 5 HELIX 5 5 ASN A 227 THR A 232 1 6 HELIX 6 6 SER A 233 LEU A 244 1 12 HELIX 7 7 GLN A 245 PHE A 247 5 3 HELIX 8 8 PRO A 254 LYS A 256 5 3 HELIX 9 9 PRO A 264 THR A 272 1 9 SHEET 1 A 4 ILE A 54 ALA A 55 0 SHEET 2 A 4 THR A 173 PRO A 185 1 O LEU A 179 N ILE A 54 SHEET 3 A 4 SER A 71 SER A 83 -1 N ALA A 72 O GLN A 184 SHEET 4 A 4 LYS A 86 ALA A 101 -1 O LYS A 86 N SER A 83 SHEET 1 B 3 TYR A 120 PHE A 125 0 SHEET 2 B 3 LEU A 132 ARG A 137 -1 O LEU A 132 N PHE A 125 SHEET 3 B 3 ASN A 154 LEU A 158 -1 O GLN A 155 N VAL A 135 SHEET 1 C 3 ILE A 216 LEU A 217 0 SHEET 2 C 3 LEU A 203 SER A 208 -1 O ILE A 207 N ILE A 216 SHEET 3 C 3 THR A 304 GLN A 309 -1 O THR A 304 N SER A 208 SHEET 1 D 3 LYS A 248 ASP A 253 0 SHEET 2 D 3 ILE A 258 GLU A 262 -1 O ILE A 258 N ASP A 253 SHEET 3 D 3 ILE A 284 LEU A 288 -1 O ILE A 285 N ILE A 261 CRYST1 64.637 91.094 49.226 90.00 97.35 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 0.015471 0.000000 0.001996 0.00000 SCALE2 0.000000 0.010978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020483 0.00000