HEADER ALLERGEN 28-JUL-05 2AHN TITLE HIGH RESOLUTION STRUCTURE OF A CHERRY ALLERGEN PRU AV 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN-LIKE PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PRUNUS AVIUM; SOURCE 3 ORGANISM_COMMON: SWEET CHERRY; SOURCE 4 ORGANISM_TAXID: 42229 KEYWDS ALLERGEN, THAUMATIN-LIKE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.DALL'ANTONIA,T.PAVKOV,H.FUCHS,H.BREITENEDER,W.KELLER REVDAT 4 25-OCT-23 2AHN 1 REMARK REVDAT 3 11-OCT-17 2AHN 1 REMARK REVDAT 2 24-FEB-09 2AHN 1 VERSN REVDAT 1 10-OCT-06 2AHN 0 JRNL AUTH Y.DALL'ANTONIA,T.PAVKOV,H.FUCHS,H.BREITENEDER,W.KELLER JRNL TITL THE HIGH-RESOLUTION CRYSTAL STRUCTURE OF AN ALLERGENIC JRNL TITL 2 THAUMATIN-LIKE PROTEIN, PRU AV 2, ISOLATED FROM RIPE JRNL TITL 3 CHERRIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.DALL'ANTONIA,T.PAVKOV,H.FUCHS,H.BREITENEDER,W.KELLER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY STRUCTURE DETERMINATION OF REMARK 1 TITL 2 THE PLANT FOOD ALLERGEN PRU AV 2 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 61 186 2005 REMARK 1 REFN ESSN 1744-3091 REMARK 1 DOI 10.1107/S1744309104033822 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.117 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.117 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2223 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 42877 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.112 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 36754 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1630 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 235 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 17049 REMARK 3 NUMBER OF RESTRAINTS : 21079 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.033 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.082 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.089 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.070 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.033 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.083 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8126 REMARK 200 MONOCHROMATOR : TRIANGULAR MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49825 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 16.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05100 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) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.16500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1THV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, CITRIC ACID, PH 3.5, REMARK 280 MICROBATCH, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 20.57500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 THR A 43 N - CA - CB ANGL. DEV. = -13.9 DEGREES REMARK 500 THR A 43 OG1 - CB - CG2 ANGL. DEV. = -14.9 DEGREES REMARK 500 THR A 43 CA - CB - CG2 ANGL. DEV. = -15.0 DEGREES REMARK 500 ARG A 50 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 50 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR A 197 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 TYR A 199 CB - CG - CD2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP A 203 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 205 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2AHN A 1 222 UNP P50694 TLP_PRUAV 24 245 SEQRES 1 A 222 ALA THR ILE SER PHE LYS ASN ASN CYS PRO TYR MET VAL SEQRES 2 A 222 TRP PRO GLY THR LEU THR SER ASP GLN LYS PRO GLN LEU SEQRES 3 A 222 SER THR THR GLY PHE GLU LEU ALA SER GLN ALA SER PHE SEQRES 4 A 222 GLN LEU ASP THR PRO VAL PRO TRP ASN GLY ARG PHE TRP SEQRES 5 A 222 ALA ARG THR GLY CYS SER THR ASP ALA SER GLY LYS PHE SEQRES 6 A 222 VAL CYS ALA THR ALA ASP CYS ALA SER GLY GLN VAL MET SEQRES 7 A 222 CYS ASN GLY ASN GLY ALA ILE PRO PRO ALA THR LEU ALA SEQRES 8 A 222 GLU PHE ASN ILE PRO ALA GLY GLY GLY GLN ASP PHE TYR SEQRES 9 A 222 ASP VAL SER LEU VAL ASP GLY PHE ASN LEU PRO MET SER SEQRES 10 A 222 VAL THR PRO GLN GLY GLY THR GLY ASP CYS LYS THR ALA SEQRES 11 A 222 SER CYS PRO ALA ASN VAL ASN ALA VAL CYS PRO SER GLU SEQRES 12 A 222 LEU GLN LYS LYS GLY SER ASP GLY SER VAL VAL ALA CYS SEQRES 13 A 222 LEU SER ALA CYS VAL LYS PHE GLY THR PRO GLN TYR CYS SEQRES 14 A 222 CYS THR PRO PRO GLN ASN THR PRO GLU THR CYS PRO PRO SEQRES 15 A 222 THR ASN TYR SER GLU ILE PHE HIS ASN ALA CYS PRO ASP SEQRES 16 A 222 ALA TYR SER TYR ALA TYR ASP ASP LYS ARG GLY THR PHE SEQRES 17 A 222 THR CYS ASN GLY GLY PRO ASN TYR ALA ILE THR PHE CYS SEQRES 18 A 222 PRO FORMUL 2 HOH *235(H2 O) HELIX 1 1 ASP A 21 LYS A 23 5 3 HELIX 2 2 ASN A 135 CYS A 140 5 6 HELIX 3 3 PRO A 141 GLU A 143 5 3 HELIX 4 4 SER A 158 GLY A 164 1 7 HELIX 5 5 THR A 165 CYS A 170 1 6 HELIX 6 6 THR A 183 CYS A 193 1 11 SHEET 1 A 5 SER A 38 ASP A 42 0 SHEET 2 A 5 THR A 2 ASN A 7 -1 N PHE A 5 O PHE A 39 SHEET 3 A 5 ASN A 215 PHE A 220 1 O TYR A 216 N SER A 4 SHEET 4 A 5 MET A 116 GLN A 121 -1 N GLN A 121 O ASN A 215 SHEET 5 A 5 ALA A 130 CYS A 132 -1 O ALA A 130 N VAL A 118 SHEET 1 B 3 TRP A 14 THR A 19 0 SHEET 2 B 3 TRP A 47 THR A 59 -1 O ARG A 50 N LEU A 18 SHEET 3 B 3 PHE A 65 THR A 69 -1 O VAL A 66 N SER A 58 SHEET 1 C 5 TRP A 14 THR A 19 0 SHEET 2 C 5 TRP A 47 THR A 59 -1 O ARG A 50 N LEU A 18 SHEET 3 C 5 LEU A 90 ILE A 95 -1 O ILE A 95 N TRP A 47 SHEET 4 C 5 GLN A 101 SER A 107 -1 O PHE A 103 N ASN A 94 SHEET 5 C 5 THR A 209 ASN A 211 -1 O CYS A 210 N ASP A 102 SHEET 1 D 2 GLN A 145 LYS A 147 0 SHEET 2 D 2 VAL A 153 CYS A 156 -1 O ALA A 155 N LYS A 146 SSBOND 1 CYS A 9 CYS A 221 1555 1555 2.05 SSBOND 2 CYS A 57 CYS A 67 1555 1555 2.05 SSBOND 3 CYS A 72 CYS A 79 1555 1555 2.11 SSBOND 4 CYS A 127 CYS A 210 1555 1555 2.04 SSBOND 5 CYS A 132 CYS A 193 1555 1555 2.05 SSBOND 6 CYS A 140 CYS A 156 1555 1555 2.06 SSBOND 7 CYS A 160 CYS A 169 1555 1555 2.11 SSBOND 8 CYS A 170 CYS A 180 1555 1555 2.05 CISPEP 1 VAL A 45 PRO A 46 0 2.45 CISPEP 2 PRO A 86 PRO A 87 0 4.39 CISPEP 3 PRO A 172 PRO A 173 0 1.46 CRYST1 44.288 41.150 58.946 90.00 107.08 90.00 P 1 21 1 2 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 0.022580 0.000000 0.006940 0.00000 SCALE2 0.000000 0.024300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017750 0.00000