HEADER ALLERGEN 16-DEC-15 5FEF TITLE CRYSTAL STRUCTURE OF THE ALLERGEN PROFILIN (ZEA M 12) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROFILIN-5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLLEN ALLERGEN ZEA M 12,ZMPRO5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_COMMON: MAIZE; SOURCE 4 ORGANISM_TAXID: 4577; SOURCE 5 TISSUE: LEAF; SOURCE 6 GENE: PRO5; 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, ZEA M 12 EXPDTA X-RAY DIFFRACTION AUTHOR I.MARES-MEJIA,A.RODRIGUEZ-ROMERO REVDAT 3 27-SEP-23 5FEF 1 REMARK REVDAT 2 08-JAN-20 5FEF 1 REMARK REVDAT 1 14-SEP-16 5FEF 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. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 12454 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 630 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 44.2500 - 3.4920 1.00 3131 178 0.1796 0.1931 REMARK 3 2 3.4920 - 2.7719 0.99 2936 167 0.2456 0.2910 REMARK 3 3 2.7719 - 2.4215 0.99 2916 131 0.2826 0.3546 REMARK 3 4 2.4215 - 2.2001 0.98 2841 154 0.2948 0.3382 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.03 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 : 0.008 1061 REMARK 3 ANGLE : 1.207 1434 REMARK 3 CHIRALITY : 0.044 154 REMARK 3 PLANARITY : 0.005 186 REMARK 3 DIHEDRAL : 14.408 396 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 5FEF 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_1000216436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 101 REMARK 200 PH : 9.0 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 MICROMAX-007 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 IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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 (%): 69.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 9.0, 1.6 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, 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 67.59750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.26550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.26550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 101.39625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.26550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.26550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.79875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.26550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.26550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 101.39625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.26550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.26550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.79875 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 67.59750 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 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 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 GLU A 45 -10.29 75.74 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FEG RELATED DB: PDB REMARK 900 RELATED ID: 5FDS RELATED DB: PDB DBREF 5FEF A 1 131 UNP Q9FR39 PROF5_MAIZE 1 131 SEQADV 5FEF GLY A 0 UNP Q9FR39 EXPRESSION TAG SEQRES 1 A 132 GLY MET SER TRP GLN ALA TYR VAL ASP ASP HIS LEU LEU SEQRES 2 A 132 CYS ASP ILE GLU GLY GLN HIS LEU SER ALA ALA ALA ILE SEQRES 3 A 132 VAL GLY HIS ASP GLY SER VAL TRP ALA GLN SER GLU ASN SEQRES 4 A 132 PHE PRO GLU LEU LYS PRO GLU GLU VAL ALA GLY MET ILE SEQRES 5 A 132 LYS ASP PHE ASP GLU PRO GLY THR LEU ALA PRO THR GLY SEQRES 6 A 132 LEU PHE VAL GLY GLY THR LYS TYR MET VAL ILE GLN GLY SEQRES 7 A 132 GLU PRO GLY VAL VAL ILE ARG GLY LYS LYS GLY THR GLY SEQRES 8 A 132 GLY ILE THR ILE LYS LYS THR GLY MET SER LEU ILE ILE SEQRES 9 A 132 GLY ILE TYR ASP GLU PRO MET THR PRO GLY GLN CYS ASN SEQRES 10 A 132 MET VAL VAL GLU ARG LEU GLY ASP TYR LEU ILE GLU GLN SEQRES 11 A 132 GLY PHE HET GOL A 201 6 HET GOL A 202 6 HET GOL A 203 6 HET GOL A 204 6 HET GOL A 205 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 5(C3 H8 O3) FORMUL 7 HOH *32(H2 O) HELIX 1 AA1 SER A 2 LEU A 11 1 10 HELIX 2 AA2 GLU A 45 GLU A 56 1 12 HELIX 3 AA3 THR A 59 GLY A 64 1 6 HELIX 4 AA4 THR A 111 GLY A 130 1 20 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 SER A 100 TYR A 106 -1 O ILE A 103 N ALA A 24 SHEET 4 AA1 7 GLY A 90 LYS A 96 -1 N LYS A 95 O ILE A 102 SHEET 5 AA1 7 VAL A 82 LYS A 87 -1 N ILE A 83 O ILE A 94 SHEET 6 AA1 7 THR A 70 GLU A 78 -1 N MET A 73 O LYS A 86 SHEET 7 AA1 7 LEU A 65 VAL A 67 -1 N LEU A 65 O TYR A 72 CISPEP 1 GLU A 108 PRO A 109 0 5.08 SITE 1 AC1 10 ASP A 53 PHE A 54 PRO A 57 GLY A 58 SITE 2 AC1 10 GLY A 77 GLU A 78 PRO A 79 GLY A 80 SITE 3 AC1 10 VAL A 82 HOH A 313 SITE 1 AC2 5 GLY A 0 MET A 1 CYS A 13 ASP A 14 SITE 2 AC2 5 LYS A 71 SITE 1 AC3 4 MET A 1 TRP A 3 MET A 73 HOH A 302 SITE 1 AC4 5 MET A 117 ARG A 121 GLU A 128 GLN A 129 SITE 2 AC4 5 HOH A 324 SITE 1 AC5 3 HIS A 28 LYS A 96 HOH A 320 CRYST1 58.531 58.531 135.195 90.00 90.00 90.00 P 43 21 2 8 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 0.017085 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007397 0.00000