10 20 30 40 50 60 70 80 1WRF - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ALLERGEN 15-OCT-04 1WRF
TITLE REFINED SOLUTION STRUCTURE OF DER F 2, THE MAJOR MITE TITLE 2 ALLERGEN FROM DERMATOPHAGOIDES FARINAE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITE GROUP 2 ALLERGEN DER F 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 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: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFLT1
KEYWDS ALLERGEN, IMMUNOGLOBULIN FOLD
EXPDTA SOLUTION NMR
NUMMDL 11
MDLTYP MINIMIZED AVERAGE
AUTHOR S.ICHIKAWA,T.TAKAI,T.INOUE,T.YUUKI,Y.OKUMURA,K.OGURA, AUTHOR 2 F.INAGAKI,H.HATANAKA
REVDAT 2 24-FEB-09 1WRF 1 VERSN REVDAT 1 19-APR-05 1WRF 0
JRNL AUTH S.ICHIKAWA,T.TAKAI,T.INOUE,T.YUUKI,Y.OKUMURA, JRNL AUTH 2 K.OGURA,F.INAGAKI,H.HATANAKA JRNL TITL NMR STUDY ON THE MAJOR MITE ALLERGEN DER F 2: ITS JRNL TITL 2 REFINED TERTIARY STRUCTURE, EPITOPES FOR JRNL TITL 3 MONOCLONAL ANTIBODIES AND CHARACTERISTICS SHARED JRNL TITL 4 BY ML PROTEIN GROUP MEMBERS JRNL REF J.BIOCHEM.(TOKYO) V. 137 255 2005 JRNL REFN ISSN 0021-924X JRNL PMID 15809326 JRNL DOI 10.1093/JB/MVI039
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.ICHIKAWA,H.HATANAKA,T.YUUKI,N.IWAMOTO,S.KOJIMA, REMARK 1 AUTH 2 C.NISHIYAMA,K.OGURA,Y.OKUMURA,F.INAGAKI REMARK 1 TITL SOLUTION STRUCTURE OF DER F 2, THE MAJOR MITE REMARK 1 TITL 2 ALLERGEN FOR ATOPIC DISEASES REMARK 1 REF J.BIOL.CHEM. V. 273 356 1998 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 9417088 REMARK 1 DOI 10.1074/JBC.273.1.356
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 1854 NOE REMARK 3 -DERIVED DISTANCE CONSTRAINTS AND 132 DIHEDRAL ANGLE REMARK 3 RESTRAINTS.
REMARK 4 REMARK 4 1WRF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-OCT-04. REMARK 100 THE RCSB ID CODE IS RCSB023912.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 328 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1ATM REMARK 210 SAMPLE CONTENTS : 2.7MM OF DER F 2 U-15N,13C; REMARK 210 20MM KH2PO4/NA2HPO4 BUFFER; REMARK 210 90% H2O, 10% D2O; 140MM N- REMARK 210 OCTYL-B-D-GLUCOSIDE; 0.01% (W/ REMARK 210 V) NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST FNOE+FCDIH+FREPEL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY.
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
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 1 ALA A 9 -69.93 -90.55 REMARK 500 1 ASN A 10 57.67 171.74 REMARK 500 1 LYS A 15 128.45 161.86 REMARK 500 1 LEU A 58 49.16 -109.20 REMARK 500 1 ASP A 59 26.64 44.40 REMARK 500 1 PRO A 66 -156.88 -82.56 REMARK 500 1 ILE A 68 -167.14 -104.67 REMARK 500 1 THR A 70 47.47 -86.74 REMARK 500 1 ASN A 71 81.86 177.75 REMARK 500 1 ALA A 98 115.72 -39.57 REMARK 500 1 LYS A 100 90.44 -50.36 REMARK 500 1 THR A 123 -86.99 -98.15 REMARK 500 2 ASN A 10 49.88 166.64 REMARK 500 2 GLU A 12 -70.99 -77.07 REMARK 500 2 LYS A 15 135.01 165.80 REMARK 500 2 ASP A 25 179.86 -51.05 REMARK 500 2 LEU A 58 45.00 -106.72 REMARK 500 2 ASP A 59 17.89 56.59 REMARK 500 2 ILE A 68 -156.82 -139.88 REMARK 500 2 THR A 70 48.19 -87.12 REMARK 500 2 ASN A 71 79.45 178.41 REMARK 500 2 LYS A 96 -10.74 75.38 REMARK 500 2 ALA A 98 113.65 -37.30 REMARK 500 2 THR A 123 -87.68 -102.70 REMARK 500 3 ALA A 9 -79.42 -60.38 REMARK 500 3 ASN A 10 37.73 -179.16 REMARK 500 3 ASN A 11 30.12 76.08 REMARK 500 3 LYS A 15 131.26 164.62 REMARK 500 3 ASP A 19 57.89 -100.48 REMARK 500 3 ASP A 25 170.53 -52.13 REMARK 500 3 PRO A 66 -158.38 -82.83 REMARK 500 3 ILE A 68 -156.41 -136.21 REMARK 500 3 THR A 70 48.06 -87.35 REMARK 500 3 ASN A 71 77.05 178.08 REMARK 500 3 ALA A 98 117.54 -36.17 REMARK 500 3 HIS A 124 75.05 54.03 REMARK 500 4 ALA A 9 -74.65 -75.33 REMARK 500 4 ASN A 10 55.64 178.49 REMARK 500 4 GLU A 12 -63.18 -98.90 REMARK 500 4 LYS A 15 141.59 156.98 REMARK 500 4 CYS A 21 -167.61 -59.65 REMARK 500 4 HIS A 22 15.30 -144.31 REMARK 500 4 SER A 24 46.72 38.14 REMARK 500 4 LEU A 58 56.97 -109.26 REMARK 500 4 ASP A 59 27.95 41.47 REMARK 500 4 PRO A 66 -157.46 -86.56 REMARK 500 4 ILE A 68 -157.66 -120.72 REMARK 500 4 THR A 70 45.08 -86.80 REMARK 500 4 ASN A 71 83.60 175.32 REMARK 500 4 ALA A 98 118.80 -34.83 REMARK 500 4 LYS A 100 89.92 -52.76 REMARK 500 4 THR A 123 -78.47 -94.62 REMARK 500 4 HIS A 124 -177.09 -56.91 REMARK 500 5 ASN A 10 -31.26 161.64 REMARK 500 5 ASN A 11 39.51 159.61 REMARK 500 5 LYS A 15 128.56 160.90 REMARK 500 5 ASP A 19 89.82 -68.15 REMARK 500 5 ASP A 59 24.76 44.01 REMARK 500 5 PRO A 66 -154.89 -81.81 REMARK 500 5 ILE A 68 -162.13 -120.44 REMARK 500 5 THR A 70 44.55 -85.76 REMARK 500 5 ASN A 71 69.65 -177.63 REMARK 500 5 LYS A 96 -17.82 77.84 REMARK 500 5 ALA A 98 116.77 -33.84 REMARK 500 5 LYS A 100 90.82 -46.93 REMARK 500 5 CYS A 119 154.60 178.88 REMARK 500 6 ASN A 10 59.23 173.98 REMARK 500 6 LYS A 15 128.54 156.59 REMARK 500 6 CYS A 21 -66.78 -108.48 REMARK 500 6 HIS A 22 -27.00 168.93 REMARK 500 6 ASP A 59 25.62 40.51 REMARK 500 6 ILE A 68 -155.15 -149.12 REMARK 500 6 THR A 70 42.41 -90.39 REMARK 500 6 ASN A 71 88.33 176.94 REMARK 500 6 ALA A 98 122.45 -28.62 REMARK 500 6 LYS A 100 92.44 -38.42 REMARK 500 7 ALA A 9 -79.52 -88.54 REMARK 500 7 ASN A 10 61.13 178.83 REMARK 500 7 ASN A 11 17.98 57.93 REMARK 500 7 LYS A 15 131.18 168.07 REMARK 500 7 CYS A 21 173.09 -47.53 REMARK 500 7 ASP A 25 157.18 -39.92 REMARK 500 7 ARG A 31 152.55 -45.26 REMARK 500 7 PRO A 66 -154.82 -82.71 REMARK 500 7 ILE A 68 -165.33 -125.79 REMARK 500 7 THR A 70 45.46 -87.11 REMARK 500 7 ASN A 71 74.17 -179.85 REMARK 500 7 ALA A 72 -5.84 -59.50 REMARK 500 7 ALA A 98 117.93 -33.15 REMARK 500 8 ASP A 7 152.49 -49.65 REMARK 500 8 ALA A 9 -76.56 -116.25 REMARK 500 8 ASN A 10 68.60 174.21 REMARK 500 8 GLU A 12 -79.20 -87.30 REMARK 500 8 LYS A 15 129.56 167.61 REMARK 500 8 ASP A 19 69.19 -105.12 REMARK 500 8 ASP A 25 156.91 -44.53 REMARK 500 8 ARG A 31 146.32 -37.74 REMARK 500 8 ASP A 59 14.99 58.00 REMARK 500 8 PRO A 66 -159.40 -83.41 REMARK 500 8 ILE A 68 -165.93 -105.93 REMARK 500 8 THR A 70 47.56 -86.74 REMARK 500 8 ASN A 71 85.87 176.72 REMARK 500 8 ASN A 93 104.88 -57.42 REMARK 500 8 ALA A 98 120.04 -29.07 REMARK 500 8 LYS A 100 91.82 -50.98 REMARK 500 8 THR A 123 -156.79 -98.28 REMARK 500 9 ASN A 10 50.86 167.20 REMARK 500 9 LYS A 15 127.30 156.96 REMARK 500 9 CYS A 21 -167.60 -76.95 REMARK 500 9 PRO A 66 -157.81 -89.17 REMARK 500 9 ILE A 68 -138.30 -140.43 REMARK 500 9 THR A 70 49.92 -92.44 REMARK 500 9 ASN A 71 81.44 177.55 REMARK 500 9 LYS A 96 3.25 -69.19 REMARK 500 9 ALA A 98 116.62 -39.38 REMARK 500 9 LYS A 100 90.88 -54.59 REMARK 500 9 CYS A 119 147.95 175.53 REMARK 500 9 THR A 123 57.22 -116.37 REMARK 500 9 HIS A 124 60.34 177.85 REMARK 500 10 ALA A 9 -82.29 -96.52 REMARK 500 10 ASN A 10 56.39 178.24 REMARK 500 10 LYS A 15 140.70 147.60 REMARK 500 10 CYS A 21 -51.52 -128.48 REMARK 500 10 HIS A 22 -84.15 166.52 REMARK 500 10 PRO A 66 -156.35 -85.04 REMARK 500 10 ILE A 68 -156.84 -127.06 REMARK 500 10 THR A 70 46.56 -88.07 REMARK 500 10 ASN A 71 83.54 175.49 REMARK 500 10 ALA A 72 1.60 -66.24 REMARK 500 10 LYS A 96 -7.23 76.21 REMARK 500 10 ALA A 98 117.60 -32.84 REMARK 500 10 LYS A 100 90.47 -50.22 REMARK 500 11 ALA A 9 -72.99 -93.65 REMARK 500 11 ASN A 10 63.48 172.50 REMARK 500 11 GLU A 12 -81.67 -57.79 REMARK 500 11 LYS A 15 126.50 167.88 REMARK 500 11 CYS A 21 155.11 -42.39 REMARK 500 11 HIS A 22 107.66 -162.87 REMARK 500 11 ASP A 59 26.72 41.71 REMARK 500 11 PRO A 66 -154.26 -81.32 REMARK 500 11 THR A 70 36.36 30.19 REMARK 500 11 ASN A 71 90.93 174.56 REMARK 500 11 LYS A 96 -4.13 67.98 REMARK 500 11 ALA A 98 118.49 -30.59 REMARK 500 11 LYS A 100 91.03 -48.33 REMARK 500 11 CYS A 119 148.07 -170.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 31 0.30 SIDE_CHAIN REMARK 500 1 ARG A 128 0.29 SIDE_CHAIN REMARK 500 2 ARG A 31 0.26 SIDE_CHAIN REMARK 500 2 ARG A 128 0.14 SIDE_CHAIN REMARK 500 3 ARG A 31 0.23 SIDE_CHAIN REMARK 500 3 ARG A 128 0.26 SIDE_CHAIN REMARK 500 4 ARG A 31 0.22 SIDE_CHAIN REMARK 500 4 ARG A 128 0.11 SIDE_CHAIN REMARK 500 5 ARG A 31 0.17 SIDE_CHAIN REMARK 500 5 ARG A 128 0.31 SIDE_CHAIN REMARK 500 6 ARG A 31 0.26 SIDE_CHAIN REMARK 500 6 ARG A 128 0.19 SIDE_CHAIN REMARK 500 7 ARG A 31 0.29 SIDE_CHAIN REMARK 500 7 ARG A 128 0.25 SIDE_CHAIN REMARK 500 8 ARG A 31 0.22 SIDE_CHAIN REMARK 500 8 ARG A 128 0.31 SIDE_CHAIN REMARK 500 9 ARG A 31 0.31 SIDE_CHAIN REMARK 500 9 ARG A 128 0.21 SIDE_CHAIN REMARK 500 10 ARG A 31 0.27 SIDE_CHAIN REMARK 500 10 ARG A 128 0.32 SIDE_CHAIN REMARK 500 11 ARG A 31 0.31 SIDE_CHAIN REMARK 500 11 ARG A 128 0.29 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AHK RELATED DB: PDB REMARK 900 THE OLD MINIMIZED AVERAGED STRUCTURE REMARK 900 RELATED ID: 1AHM RELATED DB: PDB REMARK 900 THE OLD ENSEMBLE OF TEN CONFORMERS
DBREF 1WRF A 1 129 UNP Q00855 ALL2_DERFA 18 146
SEQADV 1WRF VAL A 76 UNP Q00855 MET 93 SEE REMARK 999
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 VAL LYS CYS SEQRES 7 A 129 PRO LEU VAL LYS GLY GLN GLN TYR ASP ILE 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 ILE GLY ASP ASN GLY VAL LEU SEQRES 10 A 129 ALA CYS ALA ILE ALA THR HIS GLY LYS ILE ARG ASP
HELIX 1 1 ASN A 71 PHE A 75 5 5
SHEET 1 A 5 VAL A 5 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 LYS A 55 O THR A 107 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 MET A 17 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 TYR A 86 N PHE A 41 SHEET 1 C 2 CYS A 27 HIS A 30 0 SHEET 2 C 2 GLY A 125 ARG A 128 1 O LYS A 126 N ILE A 29
SSBOND 1 CYS A 8 CYS A 119 1555 1555 2.02 SSBOND 2 CYS A 21 CYS A 27 1555 1555 2.02 SSBOND 3 CYS A 73 CYS A 78 1555 1555 2.02
CISPEP 1 CYS A 78 PRO A 79 1 2.34 CISPEP 2 CYS A 78 PRO A 79 2 1.98 CISPEP 3 CYS A 78 PRO A 79 3 2.68 CISPEP 4 CYS A 78 PRO A 79 4 2.96 CISPEP 5 CYS A 78 PRO A 79 5 2.86 CISPEP 6 CYS A 78 PRO A 79 6 2.41 CISPEP 7 CYS A 78 PRO A 79 7 2.54 CISPEP 8 CYS A 78 PRO A 79 8 2.47 CISPEP 9 CYS A 78 PRO A 79 9 2.48 CISPEP 10 CYS A 78 PRO A 79 10 2.69 CISPEP 11 CYS A 78 PRO A 79 11 0.86
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000