PDB Short entry for 1CK1 HEADER TOXIN 26-APR-99 1CK1 TITLE STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN C3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ENTEROTOXIN TYPE C-3); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: FRI-909; SOURCE 5 SECRETION: GROWING MEDIA KEYWDS STAPHYLOCOCCAL ENTEROTOXIN, SUPERANTIGEN, ZINC, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.-I.CHI,G.A.BOHACH,C.V.STAUFFACHER REVDAT 5 03-APR-24 1CK1 1 REMARK REVDAT 4 27-DEC-23 1CK1 1 REMARK LINK REVDAT 3 24-FEB-09 1CK1 1 VERSN REVDAT 2 01-APR-03 1CK1 1 JRNL REVDAT 1 10-JUL-02 1CK1 0 JRNL AUTH Y.I.CHI,I.SADLER,L.M.JABLONSKI,S.D.CALLANTINE,C.F.DEOBALD, JRNL AUTH 2 C.V.STAUFFACHER,G.A.BOHACH JRNL TITL ZINC-MEDIATED DIMERIZATION AND ITS EFFECT ON ACTIVITY AND JRNL TITL 2 CONFORMATION OF STAPHYLOCOCCAL ENTEROTOXIN TYPE C. JRNL REF J.BIOL.CHEM. V. 277 22839 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11934896 JRNL DOI 10.1074/JBC.M201932200 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 8707 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) : 0.162 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 438 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 798 REMARK 3 BIN R VALUE (WORKING SET) : 0.1620 REMARK 3 BIN FREE R VALUE : 0.1960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.27 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 58 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 : 1944 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 83 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.10 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.241 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.82 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.100 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 3 : WAT.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CK1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000000940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : APR-93 REMARK 200 TEMPERATURE (KELVIN) : 275 REMARK 200 PH : 7.4 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 : ELLIOTT GX-20 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CCP4, XDS REMARK 200 DATA SCALING SOFTWARE : XDS, CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8889 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.11200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: MIRAS-SOLVED IDENTICAL STRUCTURE IN A DIFFERENT REMARK 200 CRYSTAL SETTING REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM PHOSPHATE (PH7.4) 2.4M AMMONIUM REMARK 280 SULFATE 1.25% PEG400, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 140.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.12500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 210.37500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 140.25000 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 210.37500 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 70.12500 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 -1.000000 0.000000 0.000000 87.40000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 280.50000 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 PHE A 44 -74.13 -96.98 REMARK 500 THR A 105 127.40 53.90 REMARK 500 SER A 106 -102.76 -74.43 REMARK 500 ASN A 141 93.10 -69.68 REMARK 500 SER A 178 -153.80 -145.90 REMARK 500 ASN A 238 -85.35 -85.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD2 REMARK 620 2 ASP A 83 OD2 102.1 REMARK 620 3 HIS A 118 ND1 118.5 121.1 REMARK 620 4 HIS A 122 NE2 94.3 98.2 117.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZNB REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ASP 9 IS FROM THE NEXT MOLECULE, THUS FORMING A REMARK 800 DIMER REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 300 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEC3 ISOFORM PURIFIED FROM STRAIN FRI209. THE SEQUENCE OF REMARK 999 THIS PROTIEN IS NOT AVAILABLE IN SEQUENCE DATABASE DBREF 1CK1 A 1 239 UNP Q06535 Q06535_STAAU 1 239 SEQRES 1 A 239 GLU SER GLN PRO ASP PRO MET PRO ASP ASP 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 LYS SEQRES 4 A 239 SER VAL ASP LYS PHE LEU ALA HIS ASP LEU ILE TYR ASN SEQRES 5 A 239 ILE ASN ASP LYS LYS LEU ASN ASN TYR ASP LYS VAL LYS SEQRES 6 A 239 THR GLU LEU LEU ASN GLU ASP LEU ALA ASN 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 SER 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 SER 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 ILE TYR LYS ASP ASN LYS SEQRES 18 A 239 MET VAL ASP SER LYS SER VAL LYS ILE GLU VAL HIS LEU SEQRES 19 A 239 THR THR LYS ASN GLY HET ZN A 300 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *83(H2 O) HELIX 1 1 PRO A 8 ASP A 10 5 3 HELIX 2 2 SER A 14 GLU A 16 5 3 HELIX 3 3 MET A 21 TYR A 28 5 8 HELIX 4 4 GLU A 71 TYR A 77 1 7 HELIX 5 5 ALA A 156 LYS A 171 1 16 HELIX 6 6 GLN A 210 TYR A 217 1 8 SHEET 1 A 3 VAL A 33 ALA A 35 0 SHEET 2 A 3 VAL A 82 GLY A 86 -1 N GLY A 86 O VAL A 33 SHEET 3 A 3 ILE A 115 LYS A 117 -1 N THR A 116 O ASP A 83 SHEET 1 B 3 ASP A 48 TYR A 51 0 SHEET 2 B 3 LYS A 63 GLU A 67 -1 N THR A 66 O LEU A 49 SHEET 3 B 3 LYS A 108 TYR A 112 1 N THR A 109 O LYS A 63 SHEET 1 C 5 ASN A 141 THR A 149 0 SHEET 2 C 5 GLN A 129 GLU A 137 -1 N VAL A 135 O THR A 142 SHEET 3 C 5 LYS A 229 THR A 236 1 N ILE A 230 O ARG A 134 SHEET 4 C 5 TYR A 181 ILE A 189 -1 N ILE A 189 O LYS A 229 SHEET 5 C 5 THR A 195 ASP A 199 -1 N TYR A 198 O ILE A 186 SHEET 1 D 2 SER A 153 THR A 155 0 SHEET 2 D 2 MET A 222 ASP A 224 -1 N VAL A 223 O VAL A 154 SSBOND 1 CYS A 93 CYS A 110 1555 1555 2.36 LINK OD2 ASP A 9 ZN ZN A 300 1545 1555 2.20 LINK OD2 ASP A 83 ZN ZN A 300 1555 1555 2.17 LINK ND1 HIS A 118 ZN ZN A 300 1555 1555 2.22 LINK NE2 HIS A 122 ZN ZN A 300 1555 1555 2.22 SITE 1 ZNB 4 ASP A 83 HIS A 118 HIS A 122 ASP A 9 SITE 1 AC1 4 ASP A 9 ASP A 83 HIS A 118 HIS A 122 CRYST1 43.700 43.700 280.500 90.00 90.00 90.00 P 41 2 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 0.022883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022883 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003565 0.00000