PDB Short entry for 2A0A HEADER ALLERGEN 16-JUN-05 2A0A TITLE SOLUTION STRUCTURE OF DER F 13, GROUP 13 ALLERGEN FROM HOUSE DUST TITLE 2 MITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DER F 13; COMPND 3 CHAIN: A; COMPND 4 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(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-M KEYWDS BETA BARREL, HELIX, ALLERGEN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.L.CHAN,Y.K.MOK REVDAT 3 06-NOV-19 2A0A 1 JRNL REMARK REVDAT 2 24-FEB-09 2A0A 1 VERSN REVDAT 1 11-APR-06 2A0A 0 JRNL AUTH S.L.CHAN,S.T.ONG,S.Y.ONG,F.T.CHEW,Y.K.MOK JRNL TITL NUCLEAR MAGNETIC RESONANCE STRUCTURE-BASED EPITOPE MAPPING JRNL TITL 2 AND MODULATION OF DUST MITE GROUP 13 ALLERGEN AS A JRNL TITL 3 HYPOALLERGEN. JRNL REF J IMMUNOL. V. 176 4852 2006 JRNL REFN ISSN 0022-1767 JRNL PMID 16585580 JRNL DOI 10.4049/JIMMUNOL.176.8.4852 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : D. A. PEARLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2A0A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033331. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM DER F 13, U-15N, 13C; 50MM REMARK 210 ACETATE BUFFER PH 4.5; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 1.0.5 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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 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 1 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES 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 1 GLU A 11 47.44 -145.92 REMARK 500 1 LYS A 12 -57.48 -154.08 REMARK 500 1 LYS A 15 13.16 56.58 REMARK 500 1 THR A 35 -152.21 -147.08 REMARK 500 1 ASN A 46 40.49 -74.52 REMARK 500 1 ASP A 47 -48.35 -153.09 REMARK 500 1 SER A 55 -142.27 -95.56 REMARK 500 1 PHE A 57 24.76 49.26 REMARK 500 1 LYS A 58 108.37 -164.34 REMARK 500 1 ALA A 75 -152.13 51.41 REMARK 500 1 ASP A 89 25.19 -170.48 REMARK 500 1 ASN A 90 -39.61 -156.19 REMARK 500 1 LYS A 100 -45.29 -155.79 REMARK 500 1 GLU A 101 84.27 167.98 REMARK 500 1 PHE A 108 84.15 -67.91 REMARK 500 1 CYS A 119 -157.36 -115.80 REMARK 500 2 SER A 3 38.17 -169.36 REMARK 500 2 LYS A 12 -41.94 66.06 REMARK 500 2 SER A 13 77.04 38.20 REMARK 500 2 LYS A 15 7.86 56.21 REMARK 500 2 THR A 35 -155.43 -125.92 REMARK 500 2 GLU A 45 79.14 -101.26 REMARK 500 2 ASN A 46 -62.60 61.24 REMARK 500 2 PHE A 51 75.91 -100.43 REMARK 500 2 LEU A 54 30.51 -91.54 REMARK 500 2 SER A 55 -136.99 -116.42 REMARK 500 2 PHE A 57 -39.84 62.00 REMARK 500 2 LYS A 65 -120.42 -120.98 REMARK 500 2 ARG A 74 -80.65 -150.26 REMARK 500 2 ASP A 76 18.99 44.89 REMARK 500 2 ASN A 90 -45.78 -149.98 REMARK 500 2 PHE A 97 28.29 -79.64 REMARK 500 2 ASP A 99 -33.51 -133.48 REMARK 500 2 LYS A 100 -50.34 -139.79 REMARK 500 2 GLU A 101 79.55 171.28 REMARK 500 2 SER A 118 109.64 -160.67 REMARK 500 2 CYS A 119 -163.70 -105.45 REMARK 500 2 ASP A 120 -49.38 -25.06 REMARK 500 3 LYS A 12 -43.29 66.36 REMARK 500 3 SER A 13 74.72 39.51 REMARK 500 3 LYS A 15 9.65 57.14 REMARK 500 3 THR A 35 -159.30 -132.64 REMARK 500 3 GLU A 45 34.22 -81.21 REMARK 500 3 ASN A 46 17.70 54.16 REMARK 500 3 ASP A 47 -56.03 -173.28 REMARK 500 3 PHE A 51 72.20 -101.88 REMARK 500 3 SER A 55 -130.73 -104.09 REMARK 500 3 PHE A 57 -34.39 60.95 REMARK 500 3 ALA A 75 -129.95 48.96 REMARK 500 3 ASP A 76 31.42 -69.51 REMARK 500 REMARK 500 THIS ENTRY HAS 188 RAMACHANDRAN OUTLIERS. 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 7 ARG A 106 0.08 SIDE CHAIN REMARK 500 10 TYR A 8 0.08 SIDE CHAIN REMARK 500 10 TYR A 128 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2A0A A 1 131 UNP Q1M2P5 Q1M2P5_DERFA 1 131 SEQRES 1 A 131 MET ALA SER ILE GLU GLY LYS TYR LYS LEU GLU LYS SER SEQRES 2 A 131 GLU LYS PHE ASP GLU PHE LEU ASP LYS LEU GLY VAL GLY SEQRES 3 A 131 PHE MET VAL LYS THR ALA ALA LYS THR LEU LYS PRO THR SEQRES 4 A 131 PHE GLU VAL ALA ILE GLU ASN ASP GLN TYR ILE PHE ARG SEQRES 5 A 131 SER LEU SER THR PHE LYS ASN THR GLU ALA LYS PHE LYS SEQRES 6 A 131 LEU GLY GLU GLU PHE GLU GLU ASP ARG ALA ASP GLY LYS SEQRES 7 A 131 ARG VAL LYS THR VAL ILE GLN LYS GLU GLY ASP ASN LYS SEQRES 8 A 131 PHE VAL GLN THR GLN PHE GLY ASP LYS GLU VAL LYS ILE SEQRES 9 A 131 ILE ARG GLU PHE ASN GLY ASP GLU VAL VAL VAL THR ALA SEQRES 10 A 131 SER CYS ASP GLY VAL THR SER VAL ARG THR TYR LYS ARG SEQRES 11 A 131 ILE HELIX 1 1 LYS A 15 GLY A 24 1 10 HELIX 2 2 GLY A 26 THR A 31 1 6 HELIX 3 3 ALA A 32 THR A 35 5 4 SHEET 1 A10 THR A 60 PHE A 64 0 SHEET 2 A10 TYR A 49 SER A 53 -1 N SER A 53 O THR A 60 SHEET 3 A10 THR A 39 ILE A 44 -1 N GLU A 41 O ARG A 52 SHEET 4 A10 GLY A 6 LEU A 10 -1 N TYR A 8 O PHE A 40 SHEET 5 A10 THR A 123 ILE A 131 -1 O ILE A 131 N LYS A 7 SHEET 6 A10 GLU A 112 SER A 118 -1 N VAL A 113 O TYR A 128 SHEET 7 A10 VAL A 102 PHE A 108 -1 N LYS A 103 O SER A 118 SHEET 8 A10 LYS A 91 GLN A 96 -1 N GLN A 94 O ILE A 104 SHEET 9 A10 LYS A 78 GLU A 87 -1 N GLN A 85 O VAL A 93 SHEET 10 A10 PHE A 70 ARG A 74 -1 N ARG A 74 O LYS A 78 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