HEADER IMMUNE SYSTEM 12-APR-00 1ET9 TITLE CRYSTAL STRUCTURE OF THE SUPERANTIGEN SPE-H FROM STREPTOCOCCUS TITLE 2 PYOGENES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPERANTIGEN SPE-H; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS BETA GRASP, OB FOLD, SUPERANTIGEN FOLD, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR V.L.ARCUS,T.PROFT,J.A.SIGRELL,H.M.BAKER,J.D.FRASER,E.N.BAKER REVDAT 5 07-FEB-24 1ET9 1 REMARK REVDAT 4 24-FEB-09 1ET9 1 VERSN REVDAT 3 01-APR-03 1ET9 1 JRNL REVDAT 2 24-MAY-00 1ET9 1 JRNL REVDAT 1 26-APR-00 1ET9 0 JRNL AUTH V.L.ARCUS,T.PROFT,J.A.SIGRELL,H.M.BAKER,J.D.FRASER,E.N.BAKER JRNL TITL CONSERVATION AND VARIATION IN SUPERANTIGEN STRUCTURE AND JRNL TITL 2 ACTIVITY HIGHLIGHTED BY THE THREE-DIMENSIONAL STRUCTURES OF JRNL TITL 3 TWO NEW SUPERANTIGENS FROM STREPTOCOCCUS PYOGENES. JRNL REF J.MOL.BIOL. V. 299 157 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10860729 JRNL DOI 10.1006/JMBI.2000.3725 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 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 : PROTEIN.TOP REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 859092.020 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 15684 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) : 0.199 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 820 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2140 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 99 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1601 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.40000 REMARK 3 B22 (A**2) : 6.13000 REMARK 3 B33 (A**2) : -2.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.22000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.650 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) : 1.010 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.790 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.070 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.920 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 46.07 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ET9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.1 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 RUH3R 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 : 44397 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 46.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, POTASSIUM SUCCINATE, SODIUM REMARK 280 PHOSPHATE, PH 5.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K 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 22.89000 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 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 LYS A 44 REMARK 465 ASP A 45 REMARK 465 VAL A 76 REMARK 465 CYS A 77 REMARK 465 GLU A 78 REMARK 465 CYS A 79 REMARK 465 PRO A 80 REMARK 465 GLY A 81 REMARK 465 LYS A 82 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 CD CE NZ REMARK 480 LYS A 40 CE NZ REMARK 480 GLN A 59 CG CD OE1 NE2 REMARK 480 LYS A 62 CD CE NZ REMARK 480 GLN A 74 CG CD OE1 NE2 REMARK 480 ARG A 83 CD NE CZ NH1 NH2 REMARK 480 GLU A 96 CG CD OE1 OE2 REMARK 480 LYS A 97 CD CE NZ REMARK 480 LYS A 98 CG CD CE NZ REMARK 480 LYS A 124 CD CE NZ REMARK 480 ARG A 148 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 151 CG CD CE NZ REMARK 480 LYS A 154 CD CE NZ REMARK 480 LYS A 165 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 TYR A 69 85.56 -156.81 REMARK 500 GLU A 96 84.71 -65.07 REMARK 500 LYS A 97 37.22 -96.03 REMARK 500 SER A 110 -34.76 72.92 REMARK 500 SER A 153 -9.49 -152.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ET6 RELATED DB: PDB REMARK 900 APO-SMEZ-2 REMARK 900 RELATED ID: 1AN8 RELATED DB: PDB REMARK 900 1AN8 IS A RELATED SUPERANTIGEN FROM STREPTOCOCCUS PYOGENES REMARK 900 RELATED ID: 1EU3 RELATED DB: PDB REMARK 900 ZN-SMEZ-2 REMARK 900 RELATED ID: 1EU4 RELATED DB: PDB REMARK 900 ZN-SPE-H DBREF 1ET9 A 1 204 UNP P0C0I6 SPEH_STRPY 33 236 SEQRES 1 A 204 ASN SER TYR ASN THR THR ASN ARG HIS ASN LEU GLU SER SEQRES 2 A 204 LEU TYR LYS HIS ASP SER ASN LEU ILE GLU ALA ASP SER SEQRES 3 A 204 ILE LYS ASN SER PRO ASP ILE VAL THR SER HIS MET LEU SEQRES 4 A 204 LYS TYR SER VAL LYS ASP LYS ASN LEU SER VAL PHE PHE SEQRES 5 A 204 GLU LYS ASP TRP ILE SER GLN GLU PHE LYS ASP LYS GLU SEQRES 6 A 204 VAL ASP ILE TYR ALA LEU SER ALA GLN GLU VAL CYS GLU SEQRES 7 A 204 CYS PRO GLY LYS ARG TYR GLU ALA PHE GLY GLY ILE THR SEQRES 8 A 204 LEU THR ASN SER GLU LYS LYS GLU ILE LYS VAL PRO VAL SEQRES 9 A 204 ASN VAL TRP ASP LYS SER LYS GLN GLN PRO PRO MET PHE SEQRES 10 A 204 ILE THR VAL ASN LYS PRO LYS VAL THR ALA GLN GLU VAL SEQRES 11 A 204 ASP ILE LYS VAL ARG LYS LEU LEU ILE LYS LYS TYR ASP SEQRES 12 A 204 ILE TYR ASN ASN ARG GLU GLN LYS TYR SER LYS GLY THR SEQRES 13 A 204 VAL THR LEU ASP LEU ASN SER GLY LYS ASP ILE VAL PHE SEQRES 14 A 204 ASP LEU TYR TYR PHE GLY ASN GLY ASP PHE ASN SER MET SEQRES 15 A 204 LEU LYS ILE TYR SER ASN ASN GLU ARG ILE ASP SER THR SEQRES 16 A 204 GLN PHE HIS VAL ASP VAL SER ILE SER FORMUL 2 HOH *78(H2 O) HELIX 1 1 ASN A 4 HIS A 17 1 14 HELIX 2 2 ASP A 55 LYS A 62 1 8 HELIX 3 3 ALA A 127 TYR A 142 1 16 HELIX 4 4 ASP A 178 LYS A 184 1 7 HELIX 5 5 ILE A 185 SER A 187 5 3 SHEET 1 A 5 LEU A 21 ILE A 27 0 SHEET 2 A 5 VAL A 66 GLN A 74 -1 N VAL A 66 O ILE A 27 SHEET 3 A 5 TYR A 84 PHE A 87 -1 N GLU A 85 O ALA A 73 SHEET 4 A 5 ASN A 47 PHE A 51 1 O ASN A 47 N TYR A 84 SHEET 5 A 5 MET A 38 SER A 42 -1 O LEU A 39 N VAL A 50 SHEET 1 B 3 LEU A 21 ILE A 27 0 SHEET 2 B 3 VAL A 66 GLN A 74 -1 N VAL A 66 O ILE A 27 SHEET 3 B 3 ILE A 90 LEU A 92 -1 O THR A 91 N ASP A 67 SHEET 1 C 5 LYS A 165 ASP A 170 0 SHEET 2 C 5 GLY A 155 LEU A 161 -1 O VAL A 157 N PHE A 169 SHEET 3 C 5 PHE A 197 ILE A 203 -1 O HIS A 198 N ASP A 160 SHEET 4 C 5 ILE A 100 ASP A 108 1 O PRO A 103 N VAL A 199 SHEET 5 C 5 LYS A 111 GLN A 112 -1 O LYS A 111 N ASP A 108 SHEET 1 D 5 LYS A 165 ASP A 170 0 SHEET 2 D 5 GLY A 155 LEU A 161 -1 O VAL A 157 N PHE A 169 SHEET 3 D 5 PHE A 197 ILE A 203 -1 O HIS A 198 N ASP A 160 SHEET 4 D 5 ILE A 100 ASP A 108 1 O PRO A 103 N VAL A 199 SHEET 5 D 5 MET A 116 VAL A 120 -1 O MET A 116 N VAL A 104 SHEET 1 E 2 LYS A 124 THR A 126 0 SHEET 2 E 2 ARG A 191 ASP A 193 -1 N ILE A 192 O VAL A 125 CRYST1 36.650 45.780 64.430 90.00 92.14 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 0.027285 0.000000 0.001020 0.00000 SCALE2 0.000000 0.021844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015532 0.00000