HEADER IMMUNE SYSTEM 28-MAY-00 1F2Q TITLE CRYSTAL STRUCTURE OF THE HUMAN HIGH-AFFINITY IGE RECEPTOR CAVEAT 1F2Q MAN B 3 HAS WRONG CHIRALITY AT ATOM C1 MAN C 3 HAS WRONG CAVEAT 2 1F2Q CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA- COMPND 3 SUBUNIT; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 6 SYNONYM: FC-EPSILON RI-ALPHA; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HI-5; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVL1392 KEYWDS IMMUNOGLOBULIN FOLD, GLYCOPROTEIN, RECEPTOR, IGE-BINDING PROTEIN, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.C.GARMAN,J.P.KINET,T.S.JARDETZKY REVDAT 4 29-JUL-20 1F2Q 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 13-JUL-11 1F2Q 1 VERSN REVDAT 2 24-FEB-09 1F2Q 1 VERSN REVDAT 1 08-JUN-00 1F2Q 0 JRNL AUTH S.C.GARMAN,J.P.KINET,T.S.JARDETZKY JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN HIGH-AFFINITY IGE RECEPTOR. JRNL REF CELL(CAMBRIDGE,MASS.) V. 95 951 1998 JRNL REFN ISSN 0092-8674 JRNL PMID 9875849 JRNL DOI 10.1016/S0092-8674(00)81719-5 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 913683.660 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 10247 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) : 0.226 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 880 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1486 REMARK 3 BIN R VALUE (WORKING SET) : 0.3770 REMARK 3 BIN FREE R VALUE : 0.4530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 158 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 : 1371 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 30.48000 REMARK 3 B22 (A**2) : -16.37000 REMARK 3 B33 (A**2) : -14.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 18.52000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.48 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 4.350 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.730 ; 6.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.600 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.090 ; 8.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 53.15 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 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAXIMUM LIKELIHOOD REFINEMENT AGAINST REMARK 3 HENDRICKSON-LATTMAN COEFFICIENT TARGETS REMARK 4 REMARK 4 1F2Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000011171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 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 : 10247 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.22600 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: DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS, SODIUM ACETATE, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.29500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.82000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.29500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.82000 REMARK 290 SMTRY3 4 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, B, C 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 VAL A 1 REMARK 465 PRO A 2 REMARK 465 GLN A 3 REMARK 465 PHE A 32 REMARK 465 GLU A 33 REMARK 465 VAL A 34 REMARK 465 SER A 35 REMARK 465 GLU A 175 REMARK 465 LYS A 176 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 ASN A 27 164.87 -24.74 REMARK 500 ASN A 57 70.57 46.13 REMARK 500 GLN A 71 21.95 -64.04 REMARK 500 VAL A 73 7.77 44.79 REMARK 500 TYR A 129 154.27 -42.72 REMARK 500 HIS A 134 4.56 42.88 REMARK 500 TRP A 156 -114.83 61.06 REMARK 500 PRO A 173 156.09 -43.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 1F2Q A 1 176 UNP P12319 FCEA_HUMAN 26 201 SEQRES 1 A 176 VAL PRO GLN LYS PRO LYS VAL SER LEU ASN PRO PRO TRP SEQRES 2 A 176 ASN ARG ILE PHE LYS GLY GLU ASN VAL THR LEU THR CYS SEQRES 3 A 176 ASN GLY ASN ASN PHE PHE GLU VAL SER SER THR LYS TRP SEQRES 4 A 176 PHE HIS ASN GLY SER LEU SER GLU GLU THR ASN SER SER SEQRES 5 A 176 LEU ASN ILE VAL ASN ALA LYS PHE GLU ASP SER GLY GLU SEQRES 6 A 176 TYR LYS CYS GLN HIS GLN GLN VAL ASN GLU SER GLU PRO SEQRES 7 A 176 VAL TYR LEU GLU VAL PHE SER ASP TRP LEU LEU LEU GLN SEQRES 8 A 176 ALA SER ALA GLU VAL VAL MET GLU GLY GLN PRO LEU PHE SEQRES 9 A 176 LEU ARG CYS HIS GLY TRP ARG ASN TRP ASP VAL TYR LYS SEQRES 10 A 176 VAL ILE TYR TYR LYS ASP GLY GLU ALA LEU LYS TYR TRP SEQRES 11 A 176 TYR GLU ASN HIS ASN ILE SER ILE THR ASN ALA THR VAL SEQRES 12 A 176 GLU ASP SER GLY THR TYR TYR CYS THR GLY LYS VAL TRP SEQRES 13 A 176 GLN LEU ASP TYR GLU SER GLU PRO LEU ASN ILE THR VAL SEQRES 14 A 176 ILE LYS ALA PRO ARG GLU LYS MODRES 1F2Q ASN A 42 ASN GLYCOSYLATION SITE MODRES 1F2Q ASN A 21 ASN GLYCOSYLATION SITE MODRES 1F2Q ASN A 166 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET MAN B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET MAN C 3 11 HET NAG A 221 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 2 MAN 2(C6 H12 O6) FORMUL 5 HOH *73(H2 O) HELIX 1 1 LYS A 59 SER A 63 5 5 HELIX 2 2 ARG A 111 TRP A 113 5 3 HELIX 3 3 THR A 142 SER A 146 5 5 SHEET 1 A 3 SER A 8 ASN A 10 0 SHEET 2 A 3 VAL A 22 THR A 25 -1 N THR A 23 O ASN A 10 SHEET 3 A 3 SER A 52 ILE A 55 -1 N LEU A 53 O LEU A 24 SHEET 1 B 5 ARG A 15 PHE A 17 0 SHEET 2 B 5 VAL A 79 PHE A 84 1 O GLU A 82 N ILE A 16 SHEET 3 B 5 GLY A 64 GLN A 69 -1 N GLY A 64 O LEU A 81 SHEET 4 B 5 LYS A 38 HIS A 41 -1 N LYS A 38 O GLN A 69 SHEET 5 B 5 SER A 44 LEU A 45 -1 O SER A 44 N HIS A 41 SHEET 1 C 3 LEU A 88 ALA A 92 0 SHEET 2 C 3 LEU A 103 GLY A 109 -1 O ARG A 106 N GLN A 91 SHEET 3 C 3 ASN A 135 ILE A 138 -1 O ILE A 136 N LEU A 105 SHEET 1 D 4 GLU A 125 ALA A 126 0 SHEET 2 D 4 VAL A 115 LYS A 122 -1 N LYS A 122 O GLU A 125 SHEET 3 D 4 GLY A 147 VAL A 155 -1 O TYR A 150 N TYR A 121 SHEET 4 D 4 LEU A 158 GLU A 161 -1 N LEU A 158 O VAL A 155 SHEET 1 E 5 GLU A 125 ALA A 126 0 SHEET 2 E 5 VAL A 115 LYS A 122 -1 N LYS A 122 O GLU A 125 SHEET 3 E 5 GLY A 147 VAL A 155 -1 O TYR A 150 N TYR A 121 SHEET 4 E 5 LEU A 165 ILE A 170 -1 N LEU A 165 O TYR A 149 SHEET 5 E 5 VAL A 96 MET A 98 1 O VAL A 97 N ILE A 170 SSBOND 1 CYS A 26 CYS A 68 1555 1555 2.04 SSBOND 2 CYS A 107 CYS A 151 1555 1555 2.05 LINK ND2 ASN A 21 C1 NAG A 221 1555 1555 1.45 LINK ND2 ASN A 42 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 166 C1 NAG C 1 1555 1555 1.47 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.39 LINK O4 NAG B 2 C1 MAN B 3 1555 1555 1.39 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.40 LINK O4 NAG C 2 C1 MAN C 3 1555 1555 1.40 CISPEP 1 ASN A 10 PRO A 11 0 -0.28 CRYST1 88.590 69.640 49.360 90.00 116.69 90.00 C 1 2 1 4 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 0.011288 0.000000 0.005675 0.00000 SCALE2 0.000000 0.014360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022675 0.00000