HEADER ALLERGEN 16-AUG-00 1FM4 TITLE CRYSTAL STRUCTURE OF THE BIRCH POLLEN ALLERGEN BET V 1L COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR POLLEN ALLERGEN BET V 1-L; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BETULA PENDULA; SOURCE 3 ORGANISM_COMMON: EUROPEAN WHITE BIRCH; SOURCE 4 ORGANISM_TAXID: 3505; SOURCE 5 TISSUE: POLLEN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMW 175-BET V 1L KEYWDS ALPHA-BETA: 6 ANTI-PARALLEL BETA STRANDS AND 3 ALPHA HELICES., KEYWDS 2 ALLERGEN EXPDTA X-RAY DIFFRACTION AUTHOR Z.MARKOVIC-HOUSLEY,M.DEGANO,D.LAMBA,E.VON ROEPENACK-LAHAYE,S.CLEMENS, AUTHOR 2 M.SUSANI,F.FERREIRA,O.SCHEINER,H.BREITENEDER REVDAT 3 07-FEB-24 1FM4 1 REMARK REVDAT 2 24-FEB-09 1FM4 1 VERSN REVDAT 1 20-DEC-02 1FM4 0 JRNL AUTH Z.MARKOVIC-HOUSLEY,M.DEGANO,D.LAMBA,E.VON ROEPENACK-LAHAYE, JRNL AUTH 2 S.CLEMENS,M.SUSANI,F.FERREIRA,O.SCHEINER,H.BREITENEDER JRNL TITL CRYSTAL STRUCTURE OF A HYPOALLERGENIC ISOFORM OF THE MAJOR JRNL TITL 2 BIRCH POLLEN ALLERGEN BET V 1 AND ITS LIKELY BIOLOGICAL JRNL TITL 3 FUNCTION AS A PLANT STEROID CARRIER JRNL REF J.MOL.BIOL. V. 325 123 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12473456 JRNL DOI 10.1016/S0022-2836(02)01197-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.SWOBODA,A.JILEK,F.FERREIRA,E.ENGEL,K.HOFFMAN-SOMMERGRUBER, REMARK 1 AUTH 2 O.SCHEINER,D.KRAFT,H.BREITENEDER,E.PITTENAUER,E.SCHMID, REMARK 1 AUTH 3 O.VICENTE,E.HEBERLE-BORS,H.AHORN,M.BREITENBACH REMARK 1 TITL ISOFORMS OF BET V 1, THE MAJOR BIRCH POLLEN ALLERGEN, REMARK 1 TITL 2 ANALYZED BY LIQUID CHROMATOGRAPHY, MASS SPECTROMETRY, AND REMARK 1 TITL 3 CDNA CLONING. REMARK 1 REF J.BIOL.CHEM. V. 270 2607 1995 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.270.6.2607 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.BREITENEDER,K.PETTENBURGER,A.BITO,R.VALENTA,D.KRAFT, REMARK 1 AUTH 2 H.RUMPOLD,O.SCHEINER,M.BREITENBACH REMARK 1 TITL THE GENE CODING FOR THE MAJOR BIRCH POLLEN ALLERGEN BETV1, REMARK 1 TITL 2 IS HIGHLY HOMOLOGOUS TO A PEA DISEASE RESISTANCE RESPONSE REMARK 1 TITL 3 GENE. REMARK 1 REF EMBO J. V. 8 1935 1989 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 807800.840 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 9658 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) : 0.197 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 999 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 991 REMARK 3 BIN R VALUE (WORKING SET) : 0.3590 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 114 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 : 1228 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : 0.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.44000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920 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) : 1.830 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.520 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.160 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.480 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 66.13 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 : CHOL.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CHOL.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT CORRECTION REMARK 4 REMARK 4 1FM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1000011704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.6 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 RU200 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 : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9670 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE, 20MM AMMONIUM REMARK 280 SULPHATE, 30%PEG-MME 2000, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 28.61500 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 28 CE NZ REMARK 480 LYS A 65 CE NZ REMARK 480 LYS A 80 CD CE NZ REMARK 480 LYS A 103 CD CE NZ REMARK 480 LYS A 129 CG CD CE NZ REMARK 480 GLU A 131 CG CD OE1 OE2 REMARK 480 GLN A 132 CG CD OE1 NE2 REMARK 480 LYS A 134 CG CD CE NZ REMARK 480 LYS A 137 CD CE NZ 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 -65.83 -92.96 REMARK 500 ASP A 93 -87.52 -109.94 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 DXC A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DXC A 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BV1 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1A (SWS P15494 L62F REMARK 900 CONFLICT) REMARK 900 RELATED ID: 1BTV RELATED DB: PDB REMARK 900 NMR STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1A (SWS P15494 L62F REMARK 900 CONFLICT) REMARK 900 RELATED ID: 1B6F RELATED DB: PDB REMARK 900 NMR STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1A DBREF 1FM4 A 1 159 UNP P43185 BEV1L_BETVE 1 159 SEQRES 1 A 159 GLY VAL PHE ASN TYR GLU THR GLU ALA THR SER VAL ILE SEQRES 2 A 159 PRO ALA ALA ARG MET PHE LYS ALA PHE ILE LEU ASP GLY SEQRES 3 A 159 ASP LYS LEU VAL PRO LYS VAL ALA PRO GLN ALA ILE SER SEQRES 4 A 159 SER VAL GLU ASN ILE GLU GLY ASN GLY GLY PRO GLY THR SEQRES 5 A 159 ILE LYS LYS ILE ASN PHE PRO GLU GLY PHE 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 VAL SEQRES 8 A 159 GLY ASP THR LEU GLU LYS ILE SER ASN GLU ILE LYS ILE SEQRES 9 A 159 VAL ALA THR PRO ASP GLY GLY CYS VAL LEU LYS ILE SER SEQRES 10 A 159 ASN LYS TYR HIS THR LYS GLY ASN 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 HET DXC A1001 28 HET DXC A1002 28 HETNAM DXC (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID HETSYN DXC DEOXYCHOLIC ACID FORMUL 2 DXC 2(C24 H40 O4) FORMUL 4 HOH *96(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 VAL A 133 HIS A 154 1 22 SHEET 1 A 7 VAL A 2 SER A 11 0 SHEET 2 A 7 CYS A 112 THR A 122 -1 O CYS A 112 N SER A 11 SHEET 3 A 7 LEU A 95 ALA A 106 -1 N GLU A 96 O HIS A 121 SHEET 4 A 7 LYS A 80 GLU A 87 -1 N TYR A 81 O ILE A 102 SHEET 5 A 7 TYR A 66 ASP A 75 -1 N LYS A 68 O GLU A 87 SHEET 6 A 7 ILE A 53 ASN A 57 -1 O LYS A 54 N ASP A 69 SHEET 7 A 7 SER A 40 GLU A 45 -1 O SER A 40 N ASN A 57 SITE 1 AC1 10 PHE A 58 PRO A 63 PHE A 64 PRO A 90 SITE 2 AC1 10 THR A 94 ILE A 98 HIS A 126 GLN A 132 SITE 3 AC1 10 SER A 136 DXC A1002 SITE 1 AC2 11 PHE A 22 ILE A 23 ASP A 69 TYR A 83 SITE 2 AC2 11 ILE A 98 ASN A 100 ASN A 118 TYR A 120 SITE 3 AC2 11 SER A 136 DXC A1001 HOH A1075 CRYST1 33.130 57.230 38.650 90.00 91.94 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 0.030184 0.000000 0.001022 0.00000 SCALE2 0.000000 0.017473 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025888 0.00000