HEADER VIRAL PROTEIN 12-NOV-13 4NKJ TITLE STRUCTURE OF INFLUENZA B VIRUS HEMAGGLUTININ AT MEMBRANE FUSION PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMAGGLUTININ HA2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HEMAGGLUTININ HA2 (UNP RESIDUES 392-541); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA B VIRUS; SOURCE 3 ORGANISM_TAXID: 1354485; SOURCE 4 GENE: HA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HA, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.NI,X.CHEN,J.SHEN,Q.WANG REVDAT 1 02-APR-14 4NKJ 0 JRNL AUTH F.NI,X.CHEN,J.SHEN,Q.WANG JRNL TITL STRUCTURAL INSIGHTS INTO THE MEMBRANE FUSION MECHANISM JRNL TITL 2 MEDIATED BY INFLUENZA VIRUS HEMAGGLUTININ. JRNL REF BIOCHEMISTRY V. 53 846 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24433110 JRNL DOI 10.1021/BI401525H REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.940 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 5609 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 264 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 37.7626 - 3.0909 0.85 2608 132 0.2582 0.2577 REMARK 3 2 3.0909 - 2.4535 0.94 2737 132 0.2467 0.2950 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 60.41 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.860 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) : 3.22780 REMARK 3 B22 (A**2) : 3.22780 REMARK 3 B33 (A**2) : -6.45550 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 : 0.015 1169 REMARK 3 ANGLE : 0.810 1472 REMARK 3 CHIRALITY : 0.050 179 REMARK 3 PLANARITY : 0.002 193 REMARK 3 DIHEDRAL : 12.832 412 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 4NKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-13. REMARK 100 THE RCSB ID CODE IS RCSB083318. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 200 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 : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5617 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 37.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.210 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 24.09000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 13.90837 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 118.29833 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 24.09000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 13.90837 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 118.29833 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 24.09000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 13.90837 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 118.29833 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 24.09000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 13.90837 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 118.29833 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 24.09000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 13.90837 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 118.29833 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 24.09000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 13.90837 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 118.29833 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 27.81674 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 236.59667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 27.81674 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 236.59667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 27.81674 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 236.59667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 27.81674 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 236.59667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 27.81674 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 236.59667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 27.81674 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 236.59667 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -107.0 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 -24.09000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 41.72510 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -48.18000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 217 LIES ON A SPECIAL POSITION. 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 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 VAL A 0 REMARK 465 GLY A 1 REMARK 465 VAL A 2 REMARK 465 ALA A 3 REMARK 465 SER A 146 REMARK 465 LEU A 147 REMARK 465 ASN A 148 REMARK 465 ASP A 149 REMARK 465 ASP A 150 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 98 61.84 -60.87 REMARK 500 ILE A 103 155.96 -45.89 REMARK 500 ASN A 105 123.15 -39.28 REMARK 500 CYS A 114 102.18 170.39 REMARK 500 GLN A 116 -94.42 67.35 REMARK 500 ALA A 124 67.57 67.02 REMARK 500 ALA A 129 -141.43 -77.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 4NKJ A 1 150 UNP S5DRP1 S5DRP1_9INFB 392 541 SEQADV 4NKJ HIS A -6 UNP S5DRP1 EXPRESSION TAG SEQADV 4NKJ HIS A -5 UNP S5DRP1 EXPRESSION TAG SEQADV 4NKJ HIS A -4 UNP S5DRP1 EXPRESSION TAG SEQADV 4NKJ HIS A -3 UNP S5DRP1 EXPRESSION TAG SEQADV 4NKJ HIS A -2 UNP S5DRP1 EXPRESSION TAG SEQADV 4NKJ HIS A -1 UNP S5DRP1 EXPRESSION TAG SEQADV 4NKJ VAL A 0 UNP S5DRP1 EXPRESSION TAG SEQADV 4NKJ SER A 107 UNP S5DRP1 CYS 498 CONFLICT SEQRES 1 A 157 HIS HIS HIS HIS HIS HIS VAL GLY VAL ALA VAL ALA ALA SEQRES 2 A 157 ASP LEU LYS SER THR GLN GLU ALA ILE ASN LYS ILE THR SEQRES 3 A 157 LYS ASN LEU ASN SER LEU SER GLU LEU GLU VAL LYS ASN SEQRES 4 A 157 LEU GLN ARG LEU SER GLY ALA MET ASP GLU LEU HIS ASN SEQRES 5 A 157 GLU ILE LEU GLU LEU ASP GLU LYS VAL ASP ASP LEU ARG SEQRES 6 A 157 ALA ASP THR ILE SER SER GLN ILE GLU LEU ALA VAL LEU SEQRES 7 A 157 LEU SER ASN GLU GLY ILE ILE ASN SER GLU ASP GLU HIS SEQRES 8 A 157 LEU LEU ALA LEU GLU ARG LYS LEU LYS LYS MET LEU GLY SEQRES 9 A 157 PRO SER ALA VAL ASP ILE GLY ASN GLY SER PHE GLU THR SEQRES 10 A 157 LYS HIS LYS CYS ASN GLN THR CYS LEU ASP ARG ILE ALA SEQRES 11 A 157 ALA GLY THR PHE ASN ALA GLY GLU PHE SER LEU PRO THR SEQRES 12 A 157 PHE ASP SER LEU ASN ILE THR ALA ALA SER LEU ASN ASP SEQRES 13 A 157 ASP FORMUL 2 HOH *27(H2 O) HELIX 1 1 ASP A 7 GLY A 76 1 70 HELIX 2 2 GLU A 81 MET A 95 1 15 HELIX 3 3 GLN A 116 ARG A 121 1 6 SSBOND 1 CYS A 114 CYS A 118 1555 1555 2.03 CRYST1 48.180 48.180 354.895 90.00 90.00 120.00 H 3 2 18 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 0.020756 0.011983 0.000000 0.00000 SCALE2 0.000000 0.023966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002818 0.00000