HEADER RNA BINDING PROTEIN 08-NOV-16 5H5N TITLE THE CRYSTAL STRUCTURE OF THE NS1 (H17N10) RNA-BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-74; COMPND 5 SYNONYM: NS1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS (A/LITTLE YELLOW-SHOULDERED SOURCE 3 BAT/GUATEMALA/060/2010(H17N10)); SOURCE 4 ORGANISM_TAXID: 1129347; SOURCE 5 STRAIN: A/LITTLE YELLOW-SHOULDERED BAT/GUATEMALA/060/2010(H17N10); SOURCE 6 GENE: NS1, NS; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS INFLUENZA VIRUS, RNA-BINDING DOMAIN, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHAO,J.QI,H.XIAO,G.F.GAO REVDAT 2 08-NOV-23 5H5N 1 JRNL REMARK REVDAT 1 23-NOV-16 5H5N 0 JRNL AUTH X.ZHAO,B.TEFSEN,Y.LI,J.QI,G.LU,Y.SHI,J.YAN,H.XIAO,G.F.GAO JRNL TITL THE NS1 GENE FROM BAT-DERIVED INFLUENZA-LIKE VIRUS H17N10 JRNL TITL 2 CAN BE RESCUED IN INFLUENZA A PR8 BACKBONE JRNL REF J.GEN.VIROL. V. 97 1797 2016 JRNL REFN ESSN 1465-2099 JRNL PMID 27217257 JRNL DOI 10.1099/JGV.0.000509 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 11821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 565 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 39.2995 - 3.1732 0.94 2841 145 0.2049 0.2420 REMARK 3 2 3.1732 - 2.5188 1.00 2860 147 0.2232 0.2468 REMARK 3 3 2.5188 - 2.2004 0.99 2818 126 0.2002 0.2967 REMARK 3 4 2.2004 - 1.9992 0.99 2737 147 0.2167 0.2782 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.230 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) : 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 : 0.009 1177 REMARK 3 ANGLE : 1.245 1583 REMARK 3 CHIRALITY : 0.087 173 REMARK 3 PLANARITY : 0.006 202 REMARK 3 DIHEDRAL : 14.706 459 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.6522 11.9012 -19.8208 REMARK 3 T TENSOR REMARK 3 T11: 0.4714 T22: 0.4332 REMARK 3 T33: 0.3981 T12: 0.0112 REMARK 3 T13: 0.0149 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 0.2864 L22: 0.1044 REMARK 3 L33: 0.2644 L12: -0.0360 REMARK 3 L13: 0.1360 L23: 0.1216 REMARK 3 S TENSOR REMARK 3 S11: -0.0021 S12: 0.0965 S13: -0.0572 REMARK 3 S21: -0.0722 S22: -0.2167 S23: -0.2394 REMARK 3 S31: 0.2138 S32: 0.0080 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9572 14.2519 -22.3244 REMARK 3 T TENSOR REMARK 3 T11: 0.4409 T22: 0.4558 REMARK 3 T33: 0.4255 T12: 0.0125 REMARK 3 T13: 0.0032 T23: 0.0424 REMARK 3 L TENSOR REMARK 3 L11: 0.0892 L22: 0.4175 REMARK 3 L33: 0.3818 L12: 0.0970 REMARK 3 L13: -0.0172 L23: -0.1483 REMARK 3 S TENSOR REMARK 3 S11: -0.0531 S12: 0.2230 S13: 0.0728 REMARK 3 S21: -0.3020 S22: 0.0697 S23: -0.0148 REMARK 3 S31: -0.0070 S32: -0.0462 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5815 25.8779 -15.0235 REMARK 3 T TENSOR REMARK 3 T11: 0.4149 T22: 0.4539 REMARK 3 T33: 0.4608 T12: 0.0127 REMARK 3 T13: 0.0294 T23: 0.0267 REMARK 3 L TENSOR REMARK 3 L11: 0.2898 L22: 0.1569 REMARK 3 L33: 0.1972 L12: -0.1732 REMARK 3 L13: -0.1869 L23: 0.1830 REMARK 3 S TENSOR REMARK 3 S11: 0.1748 S12: -0.1301 S13: 0.2961 REMARK 3 S21: 0.2019 S22: -0.1784 S23: 0.3282 REMARK 3 S31: -0.2720 S32: -0.0849 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 26 THROUGH 51 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6485 19.2591 -7.7519 REMARK 3 T TENSOR REMARK 3 T11: 0.4734 T22: 0.4610 REMARK 3 T33: 0.4756 T12: -0.0031 REMARK 3 T13: 0.0612 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.1426 L22: 0.2062 REMARK 3 L33: 0.0981 L12: -0.0139 REMARK 3 L13: -0.0821 L23: 0.1298 REMARK 3 S TENSOR REMARK 3 S11: 0.0418 S12: -0.1872 S13: 0.0175 REMARK 3 S21: 0.2293 S22: -0.0259 S23: 0.0568 REMARK 3 S31: 0.0171 S32: 0.1520 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 52 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.4397 28.5390 -16.9677 REMARK 3 T TENSOR REMARK 3 T11: 0.4428 T22: 0.5121 REMARK 3 T33: 0.6838 T12: 0.1030 REMARK 3 T13: -0.0112 T23: 0.0410 REMARK 3 L TENSOR REMARK 3 L11: 0.1859 L22: 0.0615 REMARK 3 L33: 0.0683 L12: 0.0501 REMARK 3 L13: -0.0676 L23: -0.0623 REMARK 3 S TENSOR REMARK 3 S11: 0.0443 S12: -0.5215 S13: 0.1744 REMARK 3 S21: -0.0106 S22: 0.1218 S23: 0.5462 REMARK 3 S31: -0.3716 S32: -0.6644 S33: -0.0000 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 5H5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300002078. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-13 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11847 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.6000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 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: 1AIL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.085M HEPES PH 7.5, 3.655M SODIUM REMARK 280 CHLORIDE, 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 57.46350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.92350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.92350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.19525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.92350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.92350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.73175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.92350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.92350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.19525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.92350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.92350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.73175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.46350 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: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 SER A 73 REMARK 465 MET A 74 REMARK 465 MET B 1 REMARK 465 SER B 73 REMARK 465 MET B 74 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 O HOH A 131 O HOH A 134 1.84 REMARK 500 O HOH A 132 O HOH A 135 1.88 REMARK 500 OE1 GLN A 60 O HOH A 101 1.88 REMARK 500 O HOH A 130 O HOH A 132 2.08 REMARK 500 O HOH B 102 O HOH B 116 2.12 REMARK 500 O HOH B 112 O HOH B 129 2.12 REMARK 500 NH1 ARG A 38 O HOH A 102 2.14 REMARK 500 NH2 ARG A 39 O HOH A 103 2.16 REMARK 500 O HOH A 125 O HOH A 138 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 5H5N A 1 74 UNP H6QM99 H6QM99_9INFA 1 74 DBREF 5H5N B 1 74 UNP H6QM99 H6QM99_9INFA 1 74 SEQRES 1 A 74 MET GLU PRO ASN PRO THR THR ILE ALA PHE GLN VAL ASP SEQRES 2 A 74 CYS TYR LEU TRP HIS LEU LYS LYS THR LEU SER MET MET SEQRES 3 A 74 GLY GLU VAL ASP ALA PRO PHE GLU ASP ARG LEU ARG ARG SEQRES 4 A 74 GLU GLN LYS ALA LEU LYS GLY ARG SER MET THR LEU GLY SEQRES 5 A 74 ILE ASP ILE GLN SER ALA THR GLN GLU GLY TYR TYR LYS SEQRES 6 A 74 ILE LYS SER ILE THR GLU GLU SER MET SEQRES 1 B 74 MET GLU PRO ASN PRO THR THR ILE ALA PHE GLN VAL ASP SEQRES 2 B 74 CYS TYR LEU TRP HIS LEU LYS LYS THR LEU SER MET MET SEQRES 3 B 74 GLY GLU VAL ASP ALA PRO PHE GLU ASP ARG LEU ARG ARG SEQRES 4 B 74 GLU GLN LYS ALA LEU LYS GLY ARG SER MET THR LEU GLY SEQRES 5 B 74 ILE ASP ILE GLN SER ALA THR GLN GLU GLY TYR TYR LYS SEQRES 6 B 74 ILE LYS SER ILE THR GLU GLU SER MET FORMUL 3 HOH *70(H2 O) HELIX 1 AA1 ASN A 4 MET A 26 1 23 HELIX 2 AA2 ASP A 30 GLY A 52 1 23 HELIX 3 AA3 ASP A 54 GLU A 71 1 18 HELIX 4 AA4 ASN B 4 MET B 26 1 23 HELIX 5 AA5 ASP B 30 GLY B 52 1 23 HELIX 6 AA6 ASP B 54 GLU B 72 1 19 CRYST1 53.847 53.847 114.927 90.00 90.00 90.00 P 43 21 2 16 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 0.018571 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008701 0.00000