HEADER ALLERGEN 17-DEC-15 5FEG TITLE CRYSTAL STRUCTURE OF THE DIMERIC ALLERGEN PROFILIN (HEV B 8) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROFILIN-2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: POLLEN ALLERGEN HEV B 8.0102; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEVEA BRASILIENSIS; SOURCE 3 ORGANISM_COMMON: PARA RUBBER TREE; SOURCE 4 ORGANISM_TAXID: 3981; SOURCE 5 TISSUE: LEAF; SOURCE 6 GENE: PRO2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28C KEYWDS ACTIN BINDING PROTEIN, ALLERGEN, ALLERGY, CROSS-REACTIVITY, HEV B 8 EXPDTA X-RAY DIFFRACTION AUTHOR I.MARES-MEJIA,A.RODRIGUEZ-ROMERO REVDAT 3 27-SEP-23 5FEG 1 REMARK REVDAT 2 08-JAN-20 5FEG 1 REMARK REVDAT 1 14-SEP-16 5FEG 0 JRNL AUTH I.MARES-MEJIA,S.MARTINEZ-CABALLERO,C.GARAY-CANALES, JRNL AUTH 2 P.CANO-SANCHEZ,A.TORRES-LARIOS,S.LARA-GONZALEZ,E.ORTEGA, JRNL AUTH 3 A.RODRIGUEZ-ROMERO JRNL TITL STRUCTURAL INSIGHTS INTO THE IGE MEDIATED RESPONSES INDUCED JRNL TITL 2 BY THE ALLERGENS HEV B 8 AND ZEA M 12 IN THEIR DIMERIC JRNL TITL 3 FORMS. JRNL REF SCI REP V. 6 32552 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27586352 JRNL DOI 10.1038/SREP32552 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2152: ???) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 8075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 377 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 24.3200 - 4.0372 0.92 2535 120 0.1725 0.2162 REMARK 3 2 4.0372 - 3.2068 0.95 2604 116 0.2223 0.2487 REMARK 3 3 3.2068 - 2.8021 0.94 2552 139 0.2897 0.3494 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.730 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 1957 REMARK 3 ANGLE : 1.248 2664 REMARK 3 CHIRALITY : 0.058 290 REMARK 3 PLANARITY : 0.006 354 REMARK 3 DIHEDRAL : 15.739 1142 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 5FEG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 101 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5416 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8075 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 43.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 5FDS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, PH 9.0; 2.0 M AMMONIUM REMARK 280 SULFATE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 58.22667 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 29.11333 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: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 MET B 1 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 43 CG CD CE NZ REMARK 470 SER A 44 OG REMARK 470 HIS A 55 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 LYS A 71 CG CD CE NZ REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 PHE B 42 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 SER B 44 OG REMARK 470 GLU B 45 CG CD OE1 OE2 REMARK 470 GLU B 56 CG CD OE1 OE2 REMARK 470 LEU B 60 CG CD1 CD2 REMARK 470 LEU B 65 CG CD1 CD2 REMARK 470 LYS B 71 CG CD CE NZ REMARK 470 ASP B 107 CG OD1 OD2 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 LEU B 60 OG1 THR B 63 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 10 -58.36 -143.99 REMARK 500 GLU A 16 40.20 27.77 REMARK 500 LYS A 43 -152.23 -68.57 REMARK 500 GLU A 45 -9.14 65.81 REMARK 500 ALA A 81 -55.88 -135.60 REMARK 500 GLN A 129 29.93 -77.86 REMARK 500 GLU B 16 24.48 48.70 REMARK 500 PRO B 40 -164.89 -62.60 REMARK 500 LYS B 43 -140.48 -90.11 REMARK 500 ILE B 75 -168.90 -115.29 REMARK 500 ALA B 81 -63.53 -145.51 REMARK 500 PRO B 89 32.72 -79.04 REMARK 500 PRO B 109 14.02 -62.65 REMARK 500 CYS B 115 -76.93 -41.28 REMARK 500 ASN B 116 -63.50 -18.32 REMARK 500 ARG B 121 -70.70 -44.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FDS RELATED DB: PDB REMARK 900 RELATED ID: 5FEF RELATED DB: PDB DBREF 5FEG A 1 131 UNP Q9STB6 PROF2_HEVBR 1 131 DBREF 5FEG B 1 131 UNP Q9STB6 PROF2_HEVBR 1 131 SEQRES 1 A 131 MET SER TRP GLN ALA TYR VAL ASP ASP HIS LEU MET CYS SEQRES 2 A 131 GLU ILE GLU GLY ASN HIS LEU SER ALA ALA ALA ILE ILE SEQRES 3 A 131 GLY GLN ASP GLY SER VAL TRP ALA GLN SER ALA ASN PHE SEQRES 4 A 131 PRO GLN PHE LYS SER GLU GLU ILE THR GLY ILE MET SER SEQRES 5 A 131 ASP PHE HIS GLU PRO GLY THR LEU ALA PRO THR GLY LEU SEQRES 6 A 131 TYR ILE GLY GLY THR LYS TYR MET VAL ILE GLN GLY GLU SEQRES 7 A 131 PRO GLY ALA VAL ILE ARG GLY LYS LYS GLY PRO GLY GLY SEQRES 8 A 131 VAL THR VAL LYS LYS THR ASN GLN ALA LEU ILE ILE GLY SEQRES 9 A 131 ILE TYR ASP GLU PRO MET THR PRO GLY GLN CYS ASN MET SEQRES 10 A 131 ILE VAL GLU ARG LEU GLY ASP TYR LEU ILE ASP GLN GLY SEQRES 11 A 131 TYR SEQRES 1 B 131 MET SER TRP GLN ALA TYR VAL ASP ASP HIS LEU MET CYS SEQRES 2 B 131 GLU ILE GLU GLY ASN HIS LEU SER ALA ALA ALA ILE ILE SEQRES 3 B 131 GLY GLN ASP GLY SER VAL TRP ALA GLN SER ALA ASN PHE SEQRES 4 B 131 PRO GLN PHE LYS SER GLU GLU ILE THR GLY ILE MET SER SEQRES 5 B 131 ASP PHE HIS GLU PRO GLY THR LEU ALA PRO THR GLY LEU SEQRES 6 B 131 TYR ILE GLY GLY THR LYS TYR MET VAL ILE GLN GLY GLU SEQRES 7 B 131 PRO GLY ALA VAL ILE ARG GLY LYS LYS GLY PRO GLY GLY SEQRES 8 B 131 VAL THR VAL LYS LYS THR ASN GLN ALA LEU ILE ILE GLY SEQRES 9 B 131 ILE TYR ASP GLU PRO MET THR PRO GLY GLN CYS ASN MET SEQRES 10 B 131 ILE VAL GLU ARG LEU GLY ASP TYR LEU ILE ASP GLN GLY SEQRES 11 B 131 TYR HELIX 1 AA1 SER A 2 ASP A 9 1 8 HELIX 2 AA2 GLU A 45 PHE A 54 1 10 HELIX 3 AA3 THR A 59 GLY A 64 1 6 HELIX 4 AA4 THR A 111 ILE A 127 1 17 HELIX 5 AA5 TRP B 3 HIS B 10 1 8 HELIX 6 AA6 GLU B 45 GLU B 56 1 12 HELIX 7 AA7 THR B 111 GLN B 129 1 19 SHEET 1 AA1 7 VAL A 32 GLN A 35 0 SHEET 2 AA1 7 ALA A 22 GLY A 27 -1 N ILE A 25 O ALA A 34 SHEET 3 AA1 7 ALA A 100 TYR A 106 -1 O LEU A 101 N ILE A 26 SHEET 4 AA1 7 GLY A 90 LYS A 96 -1 N GLY A 91 O TYR A 106 SHEET 5 AA1 7 VAL A 82 LYS A 87 -1 N LYS A 87 O GLY A 90 SHEET 6 AA1 7 THR A 70 VAL A 74 -1 N MET A 73 O LYS A 86 SHEET 7 AA1 7 LEU A 65 ILE A 67 -1 N LEU A 65 O TYR A 72 SHEET 1 AA2 7 VAL B 32 GLN B 35 0 SHEET 2 AA2 7 ALA B 22 GLY B 27 -1 N ILE B 25 O ALA B 34 SHEET 3 AA2 7 ALA B 100 ASP B 107 -1 O ILE B 105 N ALA B 22 SHEET 4 AA2 7 GLY B 90 LYS B 96 -1 N LYS B 95 O ILE B 102 SHEET 5 AA2 7 VAL B 82 LYS B 87 -1 N LYS B 87 O GLY B 90 SHEET 6 AA2 7 THR B 70 VAL B 74 -1 N MET B 73 O LYS B 86 SHEET 7 AA2 7 LEU B 65 ILE B 67 -1 N LEU B 65 O TYR B 72 SSBOND 1 CYS A 13 CYS B 13 1555 1555 2.02 CISPEP 1 GLU A 108 PRO A 109 0 2.38 CISPEP 2 GLU B 108 PRO B 109 0 15.15 CRYST1 58.558 58.558 87.340 90.00 90.00 120.00 P 32 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 0.017077 0.009859 0.000000 0.00000 SCALE2 0.000000 0.019719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011450 0.00000