HEADER VIRAL PROTEIN 19-JAN-14 4OIE TITLE WEST NILE VIRUS NON-STRUCTURAL PROTEIN NS1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN NS1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 963-1143; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: WEST NILE VIRUS; SOURCE 3 ORGANISM_COMMON: WNV; SOURCE 4 ORGANISM_TAXID: 11082; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21(A)+ KEYWDS NON-STRUCTURAL PROTEIN, FLAVIVIRUS, WEST NILE VIRUS, NS1, VIRAL KEYWDS 2 PROTEIN, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF KEYWDS 3 INFECTIOUS DISEASES, CSGID EXPDTA X-RAY DIFFRACTION AUTHOR M.A.EDELING,D.H.FREMONT,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS AUTHOR 2 DISEASES (CSGID) REVDAT 3 23-APR-14 4OIE 1 JRNL REVDAT 2 02-APR-14 4OIE 1 JRNL REVDAT 1 05-MAR-14 4OIE 0 JRNL AUTH M.A.EDELING,M.S.DIAMOND,D.H.FREMONT JRNL TITL STRUCTURAL BASIS OF FLAVIVIRUS NS1 ASSEMBLY AND ANTIBODY JRNL TITL 2 RECOGNITION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 4285 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24594604 JRNL DOI 10.1073/PNAS.1322036111 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17749 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) : 0.215 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 903 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 24.8572 - 3.3595 0.97 2939 134 0.1808 0.2050 REMARK 3 2 3.3595 - 2.6675 1.00 2839 150 0.2049 0.2442 REMARK 3 3 2.6675 - 2.3306 1.00 2797 158 0.2366 0.3033 REMARK 3 4 2.3306 - 2.1176 1.00 2775 160 0.2428 0.2944 REMARK 3 5 2.1176 - 1.9659 1.00 2741 160 0.2540 0.3250 REMARK 3 6 1.9659 - 1.8500 1.00 2755 141 0.3053 0.3574 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 40.51 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.99140 REMARK 3 B22 (A**2) : 1.99140 REMARK 3 B33 (A**2) : -3.98290 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.003 1441 REMARK 3 ANGLE : 0.769 1955 REMARK 3 CHIRALITY : 0.051 213 REMARK 3 PLANARITY : 0.002 252 REMARK 3 DIHEDRAL : 12.265 529 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 4OIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB084531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17797 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 24.855 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.54800 REMARK 200 R SYM FOR SHELL (I) : 0.54800 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 47.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 2K MME, 0.1 M SODIUM ACETATE, REMARK 280 PH 5.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 46.61667 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 93.23333 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 93.23333 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 46.61667 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: 1730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MSE A 168 REMARK 465 ALA A 169 REMARK 465 SER A 170 REMARK 465 MSE A 171 REMARK 465 ARG A 172 REMARK 465 GLU A 173 REMARK 465 SER A 174 REMARK 465 ASN A 175 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 LYS A 189 137.14 -175.43 REMARK 500 ASP A 197 -153.00 -142.80 REMARK 500 ASP A 208 -56.52 67.85 REMARK 500 SER A 315 36.63 -150.29 REMARK 500 LYS A 343 -80.66 -92.34 REMARK 500 THR A 344 48.37 -75.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OIG RELATED DB: PDB REMARK 900 RELATED ID: 4OII RELATED DB: PDB REMARK 900 RELATED ID: CSGID-IDP93954 RELATED DB: TARGETTRACK DBREF 4OIE A 172 352 UNP U3N977 U3N977_WNV 963 1143 SEQADV 4OIE MSE A 168 UNP U3N977 EXPRESSION TAG SEQADV 4OIE ALA A 169 UNP U3N977 EXPRESSION TAG SEQADV 4OIE SER A 170 UNP U3N977 EXPRESSION TAG SEQADV 4OIE MSE A 171 UNP U3N977 EXPRESSION TAG SEQADV 4OIE MSE A 184 UNP U3N977 ILE 975 ENGINEERED MUTATION SEQADV 4OIE MSE A 241 UNP U3N977 LEU 1032 ENGINEERED MUTATION SEQRES 1 A 185 MSE ALA SER MSE ARG GLU SER ASN THR THR GLU CYS ASP SEQRES 2 A 185 SER LYS ILE MSE GLY THR ALA VAL LYS ASN ASN LEU ALA SEQRES 3 A 185 ILE HIS SER ASP LEU SER TYR TRP ILE GLU SER ARG LEU SEQRES 4 A 185 ASN ASP THR TRP LYS LEU GLU ARG ALA VAL LEU GLY GLU SEQRES 5 A 185 VAL LYS SER CYS THR TRP PRO GLU THR HIS THR LEU TRP SEQRES 6 A 185 GLY ASP GLY ILE LEU GLU SER ASP MSE ILE ILE PRO VAL SEQRES 7 A 185 THR LEU ALA GLY PRO ARG SER ASN HIS ASN ARG ARG PRO SEQRES 8 A 185 GLY TYR LYS THR GLN ASN GLN GLY PRO TRP ASP GLU GLY SEQRES 9 A 185 ARG VAL GLU ILE ASP PHE ASP TYR CYS PRO GLY THR THR SEQRES 10 A 185 VAL THR LEU SER GLU SER CYS GLY HIS ARG GLY PRO ALA SEQRES 11 A 185 THR ARG THR THR THR GLU SER GLY LYS LEU ILE THR ASP SEQRES 12 A 185 TRP CYS CYS ARG SER CYS THR LEU PRO PRO LEU ARG TYR SEQRES 13 A 185 GLN THR ASP SER GLY CYS TRP TYR GLY MSE GLU ILE ARG SEQRES 14 A 185 PRO GLN ARG HIS ASP GLU LYS THR LEU VAL GLN SER GLN SEQRES 15 A 185 VAL ASN ALA MODRES 4OIE MSE A 184 MET SELENOMETHIONINE MODRES 4OIE MSE A 241 MET SELENOMETHIONINE MODRES 4OIE MSE A 333 MET SELENOMETHIONINE HET MSE A 184 8 HET MSE A 241 8 HET MSE A 333 8 HET GOL A 401 6 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *146(H2 O) HELIX 1 1 PRO A 226 THR A 230 5 5 HELIX 2 2 LEU A 237 MSE A 241 5 5 HELIX 3 3 PRO A 244 ALA A 248 5 5 SHEET 1 A 8 MSE A 184 LYS A 189 0 SHEET 2 A 8 LEU A 192 ASP A 197 -1 O ILE A 194 N ALA A 187 SHEET 3 A 8 TYR A 200 LEU A 206 -1 O SER A 204 N ALA A 193 SHEET 4 A 8 TRP A 210 LEU A 217 -1 O ARG A 214 N GLU A 203 SHEET 5 A 8 VAL A 273 PHE A 277 -1 O ILE A 275 N ALA A 215 SHEET 6 A 8 LEU A 321 THR A 325 -1 O ARG A 322 N ASP A 276 SHEET 7 A 8 GLY A 328 TYR A 331 -1 O TRP A 330 N TYR A 323 SHEET 8 A 8 THR A 298 ARG A 299 -1 N THR A 298 O TYR A 331 SHEET 1 B 3 THR A 284 LEU A 287 0 SHEET 2 B 3 ASP A 310 CYS A 313 1 O CYS A 313 N THR A 286 SHEET 3 B 3 ILE A 335 PRO A 337 -1 O ARG A 336 N CYS A 312 SSBOND 1 CYS A 179 CYS A 223 1555 1555 2.04 SSBOND 2 CYS A 280 CYS A 329 1555 1555 2.03 SSBOND 3 CYS A 291 CYS A 312 1555 1555 2.04 SSBOND 4 CYS A 313 CYS A 316 1555 1555 2.04 LINK C ILE A 183 N MSE A 184 1555 1555 1.33 LINK C MSE A 184 N GLY A 185 1555 1555 1.33 LINK C ASP A 240 N MSE A 241 1555 1555 1.33 LINK C MSE A 241 N ILE A 242 1555 1555 1.33 LINK C GLY A 332 N MSE A 333 1555 1555 1.33 LINK C MSE A 333 N GLU A 334 1555 1555 1.33 CISPEP 1 LEU A 318 PRO A 319 0 1.97 SITE 1 AC1 3 TRP A 201 PRO A 281 HOH A 602 CRYST1 49.710 49.710 139.850 90.00 90.00 120.00 P 31 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 0.020117 0.011614 0.000000 0.00000 SCALE2 0.000000 0.023229 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007151 0.00000