HEADER ALLERGEN 17-SEP-14 4WFU TITLE BOVINE ALLERGEN BOS D 2 IN THE TRIGONAL SPACE GROUP P3221. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALLERGEN BOS D 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 17-172; COMPND 5 SYNONYM: DANDER MAJOR ALLERGEN BDA20,DERMAL ALLERGEN BDA20, LIPOCALIN COMPND 6 ALLERGEN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS ALLERGEN, LIPOCALIN EXPDTA X-RAY DIFFRACTION AUTHOR M.H.NIEMI,J.ROUVINEN REVDAT 3 16-OCT-24 4WFU 1 REMARK REVDAT 2 10-JAN-24 4WFU 1 REMARK REVDAT 1 16-SEP-15 4WFU 0 JRNL AUTH M.H.NIEMI,M.RYTKONEN-NISSINEN,I.MIETTINEN,J.JANIS, JRNL AUTH 2 T.VIRTANEN,J.ROUVINEN JRNL TITL DIMERIZATION OF LIPOCALIN ALLERGENS. JRNL REF SCI REP V. 5 13841 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 26346541 JRNL DOI 10.1038/SREP13841 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 31890 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) : 0.211 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1595 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 38.4892 - 3.8909 0.99 2923 154 0.1808 0.1948 REMARK 3 2 3.8909 - 3.0887 0.99 2805 148 0.1968 0.2189 REMARK 3 3 3.0887 - 2.6984 0.99 2749 145 0.2394 0.2639 REMARK 3 4 2.6984 - 2.4517 1.00 2789 147 0.2327 0.2181 REMARK 3 5 2.4517 - 2.2760 0.99 2746 144 0.2145 0.2573 REMARK 3 6 2.2760 - 2.1418 0.99 2742 145 0.2180 0.2853 REMARK 3 7 2.1418 - 2.0346 0.99 2732 143 0.2042 0.2522 REMARK 3 8 2.0346 - 1.9460 0.98 2697 143 0.2278 0.2725 REMARK 3 9 1.9460 - 1.8711 0.99 2724 142 0.2922 0.3355 REMARK 3 10 1.8711 - 1.8065 0.99 2708 143 0.3278 0.3164 REMARK 3 11 1.8065 - 1.7501 0.98 2680 141 0.3975 0.3737 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 49.51 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.54730 REMARK 3 B22 (A**2) : 8.54730 REMARK 3 B33 (A**2) : -17.09460 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 : 0.006 1277 REMARK 3 ANGLE : 0.978 1736 REMARK 3 CHIRALITY : 0.076 193 REMARK 3 PLANARITY : 0.004 229 REMARK 3 DIHEDRAL : 13.473 500 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 4WFU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31990 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.74700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.640 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1BJ7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.0 M SODIUM FORMATE, PH 7.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 63.46000 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 31.73000 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 31.73000 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 63.46000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLN A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 ALA A 5 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 GLN A 73 -64.43 -96.86 REMARK 500 PHE A 82 108.56 -169.50 REMARK 500 GLU A 108 -52.29 -126.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BJ7 RELATED DB: PDB REMARK 900 BOVINE LIPOCALIN ALLERGEN BOS D 2 (ORTHORHOMBIC CRYSTAL FORM). DBREF 4WFU A 1 156 UNP Q28133 ALL2_BOVIN 17 172 SEQRES 1 A 156 GLN GLU THR PRO ALA GLU ILE ASP PRO SER LYS ILE PRO SEQRES 2 A 156 GLY GLU TRP ARG ILE ILE TYR ALA ALA ALA ASP ASN LYS SEQRES 3 A 156 ASP LYS ILE VAL GLU GLY GLY PRO LEU ARG ASN TYR TYR SEQRES 4 A 156 ARG ARG ILE GLU CYS ILE ASN ASP CYS GLU SER LEU SER SEQRES 5 A 156 ILE THR PHE TYR LEU LYS ASP GLN GLY THR CYS LEU LEU SEQRES 6 A 156 LEU THR GLU VAL ALA LYS ARG GLN GLU GLY TYR VAL TYR SEQRES 7 A 156 VAL LEU GLU PHE TYR GLY THR ASN THR LEU GLU VAL ILE SEQRES 8 A 156 HIS VAL SER GLU ASN MET LEU VAL THR TYR VAL GLU ASN SEQRES 9 A 156 TYR ASP GLY GLU ARG ILE THR LYS MET THR GLU GLY LEU SEQRES 10 A 156 ALA LYS GLY THR SER PHE THR PRO GLU GLU LEU GLU LYS SEQRES 11 A 156 TYR GLN GLN LEU ASN SER GLU ARG GLY VAL PRO ASN GLU SEQRES 12 A 156 ASN ILE GLU ASN LEU ILE LYS THR ASP ASN CYS PRO PRO FORMUL 2 HOH *90(H2 O) HELIX 1 AA1 ASP A 8 ILE A 12 5 5 HELIX 2 AA2 ASN A 25 ILE A 29 5 5 HELIX 3 AA3 THR A 124 ARG A 138 1 15 HELIX 4 AA4 PRO A 141 GLU A 143 5 3 HELIX 5 AA5 ILE A 149 ASP A 152 5 4 SHEET 1 AA1 9 TYR A 38 ILE A 45 0 SHEET 2 AA1 9 SER A 50 ASP A 59 -1 O SER A 52 N GLU A 43 SHEET 3 AA1 9 THR A 62 GLU A 74 -1 O LEU A 64 N LEU A 57 SHEET 4 AA1 9 VAL A 77 GLU A 81 -1 O VAL A 77 N GLN A 73 SHEET 5 AA1 9 THR A 85 VAL A 93 -1 O LEU A 88 N TYR A 78 SHEET 6 AA1 9 MET A 97 TYR A 105 -1 O TYR A 101 N GLU A 89 SHEET 7 AA1 9 ILE A 110 ALA A 118 -1 O LEU A 117 N LEU A 98 SHEET 8 AA1 9 ARG A 17 ALA A 23 -1 N TYR A 20 O GLY A 116 SHEET 9 AA1 9 ILE A 145 ASN A 147 -1 O GLU A 146 N ALA A 21 SSBOND 1 CYS A 44 CYS A 48 1555 1555 2.04 SSBOND 2 CYS A 63 CYS A 154 1555 1555 2.05 CRYST1 75.500 75.500 95.190 90.00 90.00 120.00 P 32 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 0.013245 0.007647 0.000000 0.00000 SCALE2 0.000000 0.015294 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010505 0.00000