HEADER ALLERGEN 02-NOV-04 1XWV TITLE STRUCTURE OF THE HOUSE DUST MITE ALLERGEN DER F 2: IMPLICATIONS FOR TITLE 2 FUNCTION AND MOLECULAR BASIS OF IGE CROSS-REACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DER F II; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MITE ALLERGEN DER F II; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DERMATOPHAGOIDES FARINAE; SOURCE 3 ORGANISM_COMMON: AMERICAN HOUSE DUST MITE; SOURCE 4 ORGANISM_TAXID: 6954; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGAPZALPHA-A KEYWDS BETA SHEETS, ALLERGEN EXPDTA X-RAY DIFFRACTION AUTHOR B.R.JOHANNESSEN,L.K.SKOV,J.S.KASTRUP,O.KRISTENSEN,C.BOLWIG, AUTHOR 2 J.N.LARSEN,M.SPANGFORT,K.LUND,M.GAJHEDE REVDAT 4 25-OCT-23 1XWV 1 REMARK REVDAT 3 24-FEB-09 1XWV 1 VERSN REVDAT 2 22-FEB-05 1XWV 1 JRNL REVDAT 1 14-DEC-04 1XWV 0 JRNL AUTH B.R.JOHANNESSEN,L.K.SKOV,J.S.KASTRUP,O.KRISTENSEN,C.BOLWIG, JRNL AUTH 2 J.N.LARSEN,M.SPANGFORT,K.LUND,M.GAJHEDE JRNL TITL STRUCTURE OF THE HOUSE DUST MITE ALLERGEN DER F 2: JRNL TITL 2 IMPLICATIONS FOR FUNCTION AND MOLECULAR BASIS OF IGE JRNL TITL 3 CROSS-REACTIVITY. JRNL REF FEBS LETT. V. 579 1208 2005 JRNL REFN ISSN 0014-5793 JRNL PMID 15710415 JRNL DOI 10.1016/J.FEBSLET.2004.11.115 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 18043 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) : 0.221 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 923 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 149 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1962 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.17000 REMARK 3 B22 (A**2) : 2.20000 REMARK 3 B33 (A**2) : -7.37000 REMARK 3 B12 (A**2) : -2.15000 REMARK 3 B13 (A**2) : -1.26000 REMARK 3 B23 (A**2) : 1.11000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 29.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XWV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 24.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : 0.24000 REMARK 200 FOR SHELL : 3.000 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: PDB ENTRY 1KTJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, POTASSIUM CITRATE, AMMONIUM REMARK 280 ACETATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 OG1 THR B 36 O HOH B 1028 2.10 REMARK 500 OD2 ASP B 4 O HOH B 1076 2.15 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 ALA A 9 -120.34 -141.42 REMARK 500 ALA B 9 -107.61 -167.93 REMARK 500 ASN B 11 25.63 98.64 REMARK 500 ALA B 50 86.82 -176.17 REMARK 500 PRO B 79 -109.59 -43.39 REMARK 500 LEU B 80 138.80 168.95 REMARK 500 LYS B 82 83.07 -49.54 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 PE3 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XPE B 1002 DBREF 1XWV A 1 129 UNP Q00855 ALL2_DERFA 10 138 DBREF 1XWV B 1 129 UNP Q00855 ALL2_DERFA 10 138 SEQRES 1 A 129 ASP GLN VAL ASP VAL LYS ASP CYS ALA ASN ASN GLU ILE SEQRES 2 A 129 LYS LYS VAL MET VAL ASP GLY CYS HIS GLY SER ASP PRO SEQRES 3 A 129 CYS ILE ILE HIS ARG GLY LYS PRO PHE THR LEU GLU ALA SEQRES 4 A 129 LEU PHE ASP ALA ASN GLN ASN THR LYS THR ALA LYS ILE SEQRES 5 A 129 GLU ILE LYS ALA SER LEU ASP GLY LEU GLU ILE ASP VAL SEQRES 6 A 129 PRO GLY ILE ASP THR ASN ALA CYS HIS PHE MET LYS CYS SEQRES 7 A 129 PRO LEU VAL LYS GLY GLN GLN TYR ASP ALA LYS TYR THR SEQRES 8 A 129 TRP ASN VAL PRO LYS ILE ALA PRO LYS SER GLU ASN VAL SEQRES 9 A 129 VAL VAL THR VAL LYS LEU VAL GLY ASP ASN GLY VAL LEU SEQRES 10 A 129 ALA CYS ALA ILE ALA THR HIS ALA LYS ILE ARG ASP SEQRES 1 B 129 ASP GLN VAL ASP VAL LYS ASP CYS ALA ASN ASN GLU ILE SEQRES 2 B 129 LYS LYS VAL MET VAL ASP GLY CYS HIS GLY SER ASP PRO SEQRES 3 B 129 CYS ILE ILE HIS ARG GLY LYS PRO PHE THR LEU GLU ALA SEQRES 4 B 129 LEU PHE ASP ALA ASN GLN ASN THR LYS THR ALA LYS ILE SEQRES 5 B 129 GLU ILE LYS ALA SER LEU ASP GLY LEU GLU ILE ASP VAL SEQRES 6 B 129 PRO GLY ILE ASP THR ASN ALA CYS HIS PHE MET LYS CYS SEQRES 7 B 129 PRO LEU VAL LYS GLY GLN GLN TYR ASP ALA LYS TYR THR SEQRES 8 B 129 TRP ASN VAL PRO LYS ILE ALA PRO LYS SER GLU ASN VAL SEQRES 9 B 129 VAL VAL THR VAL LYS LEU VAL GLY ASP ASN GLY VAL LEU SEQRES 10 B 129 ALA CYS ALA ILE ALA THR HIS ALA LYS ILE ARG ASP HET PE3 A1001 43 HET XPE B1002 31 HETNAM PE3 3,6,9,12,15,18,21,24,27,30,33,36,39- HETNAM 2 PE3 TRIDECAOXAHENTETRACONTANE-1,41-DIOL HETNAM XPE 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL HETSYN PE3 POLYETHYLENE GLYCOL HETSYN XPE DECAETHYLENE GLYCOL FORMUL 3 PE3 C28 H58 O15 FORMUL 4 XPE C20 H42 O11 FORMUL 5 HOH *240(H2 O) HELIX 1 1 ASN A 71 PHE A 75 5 5 HELIX 2 2 ASN B 71 PHE B 75 5 5 SHEET 1 A 5 LYS A 6 ASP A 7 0 SHEET 2 A 5 GLY A 115 ALA A 122 -1 O ILE A 121 N LYS A 6 SHEET 3 A 5 VAL A 104 GLY A 112 -1 N LEU A 110 O LEU A 117 SHEET 4 A 5 LYS A 51 LEU A 58 -1 N GLU A 53 O LYS A 109 SHEET 5 A 5 LEU A 61 ILE A 63 -1 O LEU A 61 N LEU A 58 SHEET 1 B 3 ILE A 13 VAL A 18 0 SHEET 2 B 3 PRO A 34 ASP A 42 -1 O GLU A 38 N MET A 17 SHEET 3 B 3 GLN A 85 ASN A 93 -1 O TRP A 92 N PHE A 35 SHEET 1 C 2 CYS A 27 HIS A 30 0 SHEET 2 C 2 ALA A 125 ARG A 128 1 O LYS A 126 N ILE A 29 SHEET 1 D 5 LYS B 6 ASP B 7 0 SHEET 2 D 5 GLY B 115 ALA B 122 -1 O ILE B 121 N LYS B 6 SHEET 3 D 5 VAL B 104 GLY B 112 -1 N GLY B 112 O GLY B 115 SHEET 4 D 5 LYS B 51 LEU B 58 -1 N SER B 57 O VAL B 105 SHEET 5 D 5 LEU B 61 ILE B 63 -1 O ILE B 63 N ALA B 56 SHEET 1 E 3 ILE B 13 VAL B 18 0 SHEET 2 E 3 PRO B 34 ASP B 42 -1 O LEU B 40 N LYS B 14 SHEET 3 E 3 GLN B 85 ASN B 93 -1 O TYR B 90 N LEU B 37 SHEET 1 F 2 CYS B 27 HIS B 30 0 SHEET 2 F 2 ALA B 125 ARG B 128 1 O LYS B 126 N ILE B 29 SSBOND 1 CYS A 8 CYS A 119 1555 1555 2.04 SSBOND 2 CYS A 21 CYS A 27 1555 1555 2.03 SSBOND 3 CYS A 73 CYS A 78 1555 1555 2.02 SSBOND 4 CYS B 8 CYS B 119 1555 1555 2.05 SSBOND 5 CYS B 21 CYS B 27 1555 1555 2.03 SSBOND 6 CYS B 73 CYS B 78 1555 1555 2.05 CISPEP 1 CYS A 78 PRO A 79 0 0.02 CISPEP 2 CYS B 78 PRO B 79 0 0.57 CISPEP 3 CYS B 78 PRO B 79 0 -0.21 SITE 1 AC1 19 ASP A 4 VAL A 18 CYS A 27 PHE A 35 SITE 2 AC1 19 LEU A 37 ILE A 54 ASP A 64 PRO A 66 SITE 3 AC1 19 ALA A 88 TYR A 90 TRP A 92 PRO A 95 SITE 4 AC1 19 ILE A 97 VAL A 108 ALA A 122 HIS A 124 SITE 5 AC1 19 ALA A 125 ILE B 97 PRO B 99 SITE 1 AC2 12 ASP B 4 CYS B 27 ILE B 29 PHE B 35 SITE 2 AC2 12 LEU B 37 ALA B 39 ILE B 52 TYR B 90 SITE 3 AC2 12 TRP B 92 ALA B 122 THR B 123 HIS B 124 CRYST1 25.712 47.638 48.275 85.98 75.90 82.76 P 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 0.038892 -0.004941 -0.009575 0.00000 SCALE2 0.000000 0.021160 -0.000867 0.00000 SCALE3 0.000000 0.000000 0.021376 0.00000