HEADER TOXIN 20-JUL-95 1SE2 TITLE STAPHYLOCOCCAL ENTEROTOXIN C2, MONOCLINIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: STAPHYLOCOCCAL ENTEROTOXIN C2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SEC2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280 KEYWDS ENTEROTOXIN, SUPERANTIGEN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SWAMINATHAN,M.SAX REVDAT 4 23-OCT-24 1SE2 1 REMARK REVDAT 3 05-JUN-24 1SE2 1 REMARK REVDAT 2 24-FEB-09 1SE2 1 VERSN REVDAT 1 08-MAR-96 1SE2 0 JRNL AUTH S.SWAMINATHAN,W.FUREY,J.PLETCHER,M.SAX JRNL TITL RESIDUES DEFINING V BETA SPECIFICITY IN STAPHYLOCOCCAL JRNL TITL 2 ENTEROTOXINS. JRNL REF NAT.STRUCT.BIOL. V. 2 680 1995 JRNL REFN ISSN 1072-8368 JRNL PMID 7552730 JRNL DOI 10.1038/NSB0895-680 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.SWAMINATHAN,W.FUREY,J.PLETCHER,M.SAX REMARK 1 TITL CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN B, A REMARK 1 TITL 2 SUPERANTIGEN REMARK 1 REF NATURE V. 359 801 1992 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.0 REMARK 3 NUMBER OF REFLECTIONS : 5535 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.320 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1914 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 2.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SE2 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_1000176337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1994 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7124 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05270 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 34.96000 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 VAL A 101 REMARK 465 GLY A 102 REMARK 465 LYS A 103 REMARK 465 VAL A 104 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 SER A 2 N - CA - C ANGL. DEV. = 17.8 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = 7.0 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 SER A 2 111.59 -0.67 REMARK 500 PRO A 4 -177.33 -58.86 REMARK 500 PRO A 8 -70.31 -44.92 REMARK 500 GLU A 10 -31.14 -168.77 REMARK 500 THR A 20 110.40 49.36 REMARK 500 ASP A 30 59.19 33.90 REMARK 500 TYR A 32 174.83 167.83 REMARK 500 PHE A 44 -63.19 -104.50 REMARK 500 ASP A 55 91.72 -61.79 REMARK 500 LYS A 56 33.82 -65.04 REMARK 500 LYS A 57 -138.78 -150.60 REMARK 500 LYS A 59 89.99 -9.28 REMARK 500 ASN A 70 -177.84 -178.52 REMARK 500 ASP A 79 -4.30 89.64 REMARK 500 TYR A 85 116.34 -165.63 REMARK 500 CYS A 93 136.43 -170.42 REMARK 500 TYR A 94 154.22 -40.02 REMARK 500 PHE A 95 72.11 -117.91 REMARK 500 SER A 96 -161.57 -54.00 REMARK 500 SER A 97 -25.84 -18.46 REMARK 500 GLU A 119 109.17 -53.51 REMARK 500 GLN A 129 49.25 15.02 REMARK 500 ASN A 130 93.10 -25.81 REMARK 500 VAL A 131 113.11 -32.60 REMARK 500 ASN A 138 77.59 59.97 REMARK 500 LYS A 139 -91.15 60.27 REMARK 500 ARG A 140 130.03 -18.05 REMARK 500 SER A 144 121.32 -171.18 REMARK 500 ASN A 177 -72.17 -76.82 REMARK 500 SER A 178 -133.38 -141.65 REMARK 500 VAL A 223 -149.80 -137.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 STRANDS 2 A AND 3 A TAKE PART IN BOTH SHEETS A AND B AND REMARK 700 ARE REPEATED AS STRANDS 4 B AND 3 B IN SHEET RECORDS. DBREF 1SE2 A 1 239 UNP P34071 ENTC2_STAAU 28 266 SEQRES 1 A 239 GLU SER GLN PRO ASP PRO THR PRO ASP GLU LEU HIS LYS SEQRES 2 A 239 SER SER GLU PHE THR GLY THR MET GLY ASN MET LYS TYR SEQRES 3 A 239 LEU TYR ASP ASP HIS TYR VAL SER ALA THR LYS VAL MET SEQRES 4 A 239 SER VAL ASP LYS PHE LEU ALA HIS ASP LEU ILE TYR ASN SEQRES 5 A 239 ILE SER ASP LYS LYS LEU LYS ASN TYR ASP LYS VAL LYS SEQRES 6 A 239 THR GLU LEU LEU ASN GLU ASP LEU ALA LYS LYS TYR LYS SEQRES 7 A 239 ASP GLU VAL VAL ASP VAL TYR GLY SER ASN TYR TYR VAL SEQRES 8 A 239 ASN CYS TYR PHE SER SER LYS ASP ASN VAL GLY LYS VAL SEQRES 9 A 239 THR GLY GLY LYS THR CYS MET TYR GLY GLY ILE THR LYS SEQRES 10 A 239 HIS GLU GLY ASN HIS PHE ASP ASN GLY ASN LEU GLN ASN SEQRES 11 A 239 VAL LEU ILE ARG VAL TYR GLU ASN LYS ARG ASN THR ILE SEQRES 12 A 239 SER PHE GLU VAL GLN THR ASP LYS LYS SER VAL THR ALA SEQRES 13 A 239 GLN GLU LEU ASP ILE LYS ALA ARG ASN PHE LEU ILE ASN SEQRES 14 A 239 LYS LYS ASN LEU TYR GLU PHE ASN SER SER PRO TYR GLU SEQRES 15 A 239 THR GLY TYR ILE LYS PHE ILE GLU ASN ASN GLY ASN THR SEQRES 16 A 239 PHE TRP TYR ASP MET MET PRO ALA PRO GLY ASP LYS PHE SEQRES 17 A 239 ASP GLN SER LYS TYR LEU MET MET TYR ASN ASP ASN LYS SEQRES 18 A 239 THR VAL ASP SER LYS SER VAL LYS ILE GLU VAL HIS LEU SEQRES 19 A 239 THR THR LYS ASN GLY HELIX 1 1 LYS A 13 GLU A 16 1 4 HELIX 2 2 MET A 21 TYR A 28 1 8 HELIX 3 3 ASN A 70 TYR A 77 1 8 HELIX 4 4 ALA A 156 LYS A 171 1 16 HELIX 5 5 GLN A 210 LEU A 214 1 5 HELIX 6 6 MET A 215 ASP A 219 5 5 SHEET 1 A 3 VAL A 33 VAL A 38 0 SHEET 2 A 3 VAL A 81 TYR A 90 -1 N GLY A 86 O VAL A 33 SHEET 3 A 3 LYS A 108 LYS A 117 -1 N THR A 116 O ASP A 83 SHEET 1 B 4 ASP A 48 ASN A 52 0 SHEET 2 B 4 ASP A 62 GLU A 67 -1 N THR A 66 O LEU A 49 SHEET 3 B 4 LYS A 108 LYS A 117 1 N THR A 109 O LYS A 63 SHEET 4 B 4 VAL A 81 TYR A 90 1 N TYR A 89 O CYS A 110 SHEET 1 C 5 ARG A 140 GLU A 146 0 SHEET 2 C 5 ASN A 130 GLU A 137 -1 N VAL A 135 O THR A 142 SHEET 3 C 5 LYS A 229 THR A 236 1 N VAL A 232 O ARG A 134 SHEET 4 C 5 TYR A 181 GLU A 190 -1 N ILE A 189 O LYS A 229 SHEET 5 C 5 ASN A 194 MET A 200 -1 N TYR A 198 O ILE A 186 SSBOND 1 CYS A 93 CYS A 110 1555 1555 2.05 CRYST1 43.430 69.920 42.220 90.00 90.10 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 0.023026 0.000000 0.000040 0.00000 SCALE2 0.000000 0.014302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023685 0.00000