HEADER BACTERIAL SUPERANTIGEN 27-JUN-97 1AN8 TITLE CRYSTAL STRUCTURE OF THE STREPTOCOCCAL SUPERANTIGEN SPE-C COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTOCOCCAL PYROGENIC EXOTOXIN C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SPE-C; COMPND 5 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_VECTOR_TYPE: BACTERIAL KEYWDS BACTERIAL SUPERANTIGEN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ROUSSEL,E.N.BAKER REVDAT 3 07-FEB-24 1AN8 1 REMARK REVDAT 2 24-FEB-09 1AN8 1 VERSN REVDAT 1 29-APR-98 1AN8 0 JRNL AUTH A.ROUSSEL,B.F.ANDERSON,H.M.BAKER,J.D.FRASER,E.N.BAKER JRNL TITL CRYSTAL STRUCTURE OF THE STREPTOCOCCAL SUPERANTIGEN SPE-C: JRNL TITL 2 DIMERIZATION AND ZINC BINDING SUGGEST A NOVEL MODE OF JRNL TITL 3 INTERACTION WITH MHC CLASS II MOLECULES. JRNL REF NAT.STRUCT.BIOL. V. 4 635 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9253413 JRNL DOI 10.1038/NSB0897-635 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 16645 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1221 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1740 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1710 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 7.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1221 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17866 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1702 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 34.317 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; 1.200 ; 1739 REMARK 3 BOND ANGLES (DEGREES) : 1.266 ; 1.300 ; 2339 REMARK 3 TORSION ANGLES (DEGREES) : 22.127; 0.000 ; 1031 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.009 ; 2.000 ; 52 REMARK 3 GENERAL PLANES (A) : 0.014 ; 5.000 ; 246 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 2.668 ; 4.000 ; 1739 REMARK 3 NON-BONDED CONTACTS (A) : 0.033 ; 10.000; 27 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : TRONRUD METHOD REMARK 3 KSOL : 0.73 REMARK 3 BSOL : 189.6 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL V1.0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: X-PLOR ALSO WAS USED. RESIDUE 3 HAS NO REMARK 3 REPORTED DENSITY. REMARK 4 REMARK 4 1AN8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : APR-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : FILM REMARK 200 DETECTOR MANUFACTURER : FILM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (ROTAVATA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17866 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 2.7 M REMARK 280 AMMONIUM SULFATE IN 0.1 M TRIS/HCL BUFFER AT PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 84.43500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.70500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 126.65250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.70500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.70500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.21750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.70500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.70500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 126.65250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.70500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.70500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.21750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 84.43500 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: DIMERIC 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 BIOMT1 2 0.000000 -1.000000 0.000000 75.41000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 75.41000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 84.43500 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 ASP A 1 REMARK 465 SER A 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 3 CG 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 ASP A 26 70.53 54.24 REMARK 500 THR A 33 -166.03 -115.87 REMARK 500 ASP A 66 -2.82 80.76 REMARK 500 HIS A 81 -127.91 59.72 REMARK 500 ASN A 177 -128.14 48.50 REMARK 500 SER A 200 -65.11 -102.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZNA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: THIS SITE ALSO INCLUDES HIS 81 FROM A SYMMETRY REMARK 800 -RELATED MOLECULE. REMARK 800 REMARK 800 SITE_IDENTIFIER: ZNB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: THIS SITE ALSO INCLUDES HIS 35 AND GLU 54 FROM A REMARK 800 SYMMETRY-RELATED MOLECULE. DBREF 1AN8 A 1 208 UNP P13380 SPEC_STRPY 28 235 SEQRES 1 A 208 ASP SER LYS LYS ASP ILE SER ASN VAL LYS SER ASP LEU SEQRES 2 A 208 LEU TYR ALA TYR THR ILE THR PRO TYR ASP TYR LYS ASP SEQRES 3 A 208 CYS ARG VAL ASN PHE SER THR THR HIS THR LEU ASN ILE SEQRES 4 A 208 ASP THR GLN LYS TYR ARG GLY LYS ASP TYR TYR ILE SER SEQRES 5 A 208 SER GLU MET SER TYR GLU ALA SER GLN LYS PHE LYS ARG SEQRES 6 A 208 ASP ASP HIS VAL ASP VAL PHE GLY LEU PHE TYR ILE LEU SEQRES 7 A 208 ASN SER HIS THR GLY GLU TYR ILE TYR GLY GLY ILE THR SEQRES 8 A 208 PRO ALA GLN ASN ASN LYS VAL ASN HIS LYS LEU LEU GLY SEQRES 9 A 208 ASN LEU PHE ILE SER GLY GLU SER GLN GLN ASN LEU ASN SEQRES 10 A 208 ASN LYS ILE ILE LEU GLU LYS ASP ILE VAL THR PHE GLN SEQRES 11 A 208 GLU ILE ASP PHE LYS ILE ARG LYS TYR LEU MET ASP ASN SEQRES 12 A 208 TYR LYS ILE TYR ASP ALA THR SER PRO TYR VAL SER GLY SEQRES 13 A 208 ARG ILE GLU ILE GLY THR LYS ASP GLY LYS HIS GLU GLN SEQRES 14 A 208 ILE ASP LEU PHE ASP SER PRO ASN GLU GLY THR ARG SER SEQRES 15 A 208 ASP ILE PHE ALA LYS TYR LYS ASP ASN ARG ILE ILE ASN SEQRES 16 A 208 MET LYS ASN PHE SER HIS PHE ASP ILE TYR LEU GLU LYS FORMUL 2 HOH *140(H2 O) HELIX 1 1 ILE A 6 TYR A 17 1 12 HELIX 2 2 GLN A 42 ARG A 45 1 4 HELIX 3 3 TYR A 57 LYS A 62 1 6 HELIX 4 4 PHE A 129 TYR A 144 1 16 HELIX 5 5 ARG A 181 ASP A 190 1 10 HELIX 6 6 MET A 196 ASN A 198 5 3 SHEET 1 A 3 TYR A 22 TYR A 24 0 SHEET 2 A 3 VAL A 69 GLY A 73 -1 N GLY A 73 O TYR A 22 SHEET 3 A 3 ILE A 90 PRO A 92 -1 N THR A 91 O ASP A 70 SHEET 1 B 4 GLY A 83 TYR A 87 0 SHEET 2 B 4 TYR A 50 GLU A 54 1 N TYR A 50 O GLU A 84 SHEET 3 B 4 THR A 36 ASP A 40 -1 N ILE A 39 O ILE A 51 SHEET 4 B 4 VAL A 29 SER A 32 -1 N PHE A 31 O ASN A 38 SHEET 1 C 4 GLY A 104 ILE A 108 0 SHEET 2 C 4 PHE A 199 GLU A 207 1 N PHE A 202 O ASN A 105 SHEET 3 C 4 SER A 155 THR A 162 -1 N GLY A 161 O SER A 200 SHEET 4 C 4 HIS A 167 ASP A 171 -1 N ILE A 170 O ILE A 158 SHEET 1 D 2 ILE A 126 THR A 128 0 SHEET 2 D 2 ILE A 193 ASN A 195 -1 N ILE A 194 O VAL A 127 SITE 1 ZNA 3 HIS A 167 HIS A 201 ASP A 203 SITE 1 ZNB 2 HIS A 35 GLU A 54 CRYST1 75.410 75.410 168.870 90.00 90.00 90.00 P 43 21 2 8 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 0.013261 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005922 0.00000