HEADER ALLERGEN 06-OCT-99 1QMR TITLE BIRCH POLLEN ALLERGEN BET V 1 MUTANT N28T, K32Q, E45S, P108G COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR POLLEN ALLERGEN BET V 1-A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BET V 1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BETULA VERRUCOSA; SOURCE 3 ORGANISM_COMMON: WHITE BIRCH; SOURCE 4 ORGANISM_TAXID: 3505; SOURCE 5 CELL: POLLEN; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 GENE: BET V 1 1.2801; SOURCE 8 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS ALLERGEN, PATHOGENESIS-RELATED PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.HENRIKSEN,J.O.HOLM,M.D.SPANGFORT,M.GAJHEDE REVDAT 6 13-DEC-23 1QMR 1 REMARK REVDAT 5 09-OCT-19 1QMR 1 JRNL REVDAT 4 05-JUL-17 1QMR 1 REMARK REVDAT 3 24-FEB-09 1QMR 1 VERSN REVDAT 2 21-OCT-04 1QMR 1 JRNL REVDAT 1 12-OCT-00 1QMR 0 JRNL AUTH J.HOLM,M.GAJHEDE,M.FERRERAS,A.HENRIKSEN,H.IPSEN,J.N.LARSEN, JRNL AUTH 2 L.LUND,H.JACOBI,A.MILLNER,P.A.WURTZEN,M.D.SPANGFORT JRNL TITL ALLERGY VACCINE ENGINEERING: EPITOPE MODULATION OF JRNL TITL 2 RECOMBINANT BET V 1 REDUCES IGE BINDING BUT RETAINS PROTEIN JRNL TITL 3 FOLDING PATTERN FOR INDUCTION OF PROTECTIVE JRNL TITL 4 BLOCKING-ANTIBODY RESPONSES. JRNL REF J IMMUNOL. V. 173 5258 2004 JRNL REFN ISSN 0022-1767 JRNL PMID 15470071 JRNL DOI 10.4049/JIMMUNOL.173.8.5258 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.GAJHEDE,P.OSMARK,F.M.POULSEN,H.IPSEN,J.N.LARSEN, REMARK 1 AUTH 2 R.J.J.VAN NEERVEN,C.SCHOU,H.LOWENSTEIN,M.D.SPANGFORT REMARK 1 TITL X-RAY AND NMR STRUCTURE OF BET V 1, THE ORIGIN OF BIRCH REMARK 1 TITL 2 POLLEN ALLERGY REMARK 1 REF NAT.STRUCT.BIOL. V. 3 1040 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 8946858 REMARK 1 DOI 10.1038/NSB1296-1040 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 248643.490 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 7797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 407 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 981 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 56 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1223 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : -4.50000 REMARK 3 B33 (A**2) : 4.03000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 38.76 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QMR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1290004195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 287.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7832 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 34.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13500 REMARK 200 FOR SHELL : 9.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 0.5 REMARK 200 STARTING MODEL: PDB ENTRY 1BV1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.77400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.77400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 16.17350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.09800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 16.17350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.09800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.77400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 16.17350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.09800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.77400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 16.17350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.09800 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 74.19600 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 CHAIN A ENGINEERED MUTATION ASN28THR, LYS32GLN, GLU45SER, REMARK 400 PRO108GLY 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 ILE A 23 -61.86 -96.39 REMARK 500 ASP A 93 -84.17 43.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BTV RELATED DB: PDB REMARK 900 STRUCTURE OF BET V 1, NMR, 20 STRUCTURES REMARK 900 RELATED ID: 1BV1 RELATED DB: PDB REMARK 900 BIRCH POLLEN ALLERGEN BET V 1 REMARK 900 RELATED ID: 1B6F RELATED DB: PDB REMARK 900 BIRCH POLLEN ALLERGEN BET V 1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE LEU 62 SWS P15494 PHE 62 CONFLICT IS A KNOWN REMARK 999 VARIANT FROM THE SWISSPROT SEQUENCE TAKEN FROM REMARK 999 REFERENCE: REMARK 999 BREITENEDER H.,PETTENBURGER K.,BITO A.,VALENTA R., REMARK 999 KRAFT D.,RUMPOLD H.,SCHEINER O.,BREITENBACH M. REMARK 999 EMBO J. 8:1935-1938(1989). DBREF 1QMR A 1 159 UNP P15494 BV1A_BETVE 1 159 SEQADV 1QMR THR A 28 UNP P15494 ASN 28 ENGINEERED MUTATION SEQADV 1QMR GLN A 32 UNP P15494 LYS 32 ENGINEERED MUTATION SEQADV 1QMR SER A 45 UNP P15494 GLU 45 ENGINEERED MUTATION SEQADV 1QMR GLY A 108 UNP P15494 PRO 108 ENGINEERED MUTATION SEQADV 1QMR LEU A 62 UNP P15494 PHE 62 CONFLICT SEQRES 1 A 159 GLY VAL PHE ASN TYR GLU THR GLU THR THR SER VAL ILE SEQRES 2 A 159 PRO ALA ALA ARG LEU PHE LYS ALA PHE ILE LEU ASP GLY SEQRES 3 A 159 ASP THR LEU PHE PRO GLN VAL ALA PRO GLN ALA ILE SER SEQRES 4 A 159 SER VAL GLU ASN ILE SER GLY ASN GLY GLY PRO GLY THR SEQRES 5 A 159 ILE LYS LYS ILE SER PHE PRO GLU GLY LEU PRO PHE LYS SEQRES 6 A 159 TYR VAL LYS ASP ARG VAL ASP GLU VAL ASP HIS THR ASN SEQRES 7 A 159 PHE LYS TYR ASN TYR SER VAL ILE GLU GLY GLY PRO ILE SEQRES 8 A 159 GLY ASP THR LEU GLU LYS ILE SER ASN GLU ILE LYS ILE SEQRES 9 A 159 VAL ALA THR GLY ASP GLY GLY SER ILE LEU LYS ILE SER SEQRES 10 A 159 ASN LYS TYR HIS THR LYS GLY ASP HIS GLU VAL LYS ALA SEQRES 11 A 159 GLU GLN VAL LYS ALA SER LYS GLU MET GLY GLU THR LEU SEQRES 12 A 159 LEU ARG ALA VAL GLU SER TYR LEU LEU ALA HIS SER ASP SEQRES 13 A 159 ALA TYR ASN FORMUL 2 HOH *46(H2 O) HELIX 1 1 PRO A 14 ILE A 23 1 10 HELIX 2 2 ASP A 25 ALA A 34 1 10 HELIX 3 3 LYS A 129 HIS A 154 1 26 SHEET 1 A 5 VAL A 2 SER A 11 0 SHEET 2 A 5 SER A 112 THR A 122 -1 N TYR A 120 O PHE A 3 SHEET 3 A 5 LEU A 95 ALA A 106 -1 N VAL A 105 O ILE A 113 SHEET 4 A 5 LYS A 80 VAL A 85 -1 N VAL A 85 O ILE A 98 SHEET 5 A 5 GLU A 73 ASP A 75 -1 N ASP A 75 O LYS A 80 SHEET 1 B 4 SER A 40 SER A 45 0 SHEET 2 B 4 ILE A 53 SER A 57 -1 N SER A 57 O SER A 40 SHEET 3 B 4 TYR A 66 VAL A 71 -1 N ASP A 69 O LYS A 54 SHEET 4 B 4 TYR A 83 GLY A 88 -1 N GLU A 87 O LYS A 68 CRYST1 32.347 74.196 119.548 90.00 90.00 90.00 C 2 2 21 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 0.030915 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008365 0.00000