HEADER TOXIN 20-AUG-24 9J7X TITLE CRYSTAL STRUCTURE OF QUINTUPLE MUTANT C TERMINAL FRAGMENT OF TITLE 2 CLOSTRIDIUM PERFRINGENS ENTEROTOXIN (C-CPEM19) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT-LABILE ENTEROTOXIN B CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: QUINTUPLE MUTANT C TERMINAL FRAGMENT OF CLOSTRIDIUM COMPND 5 PERFRINGENS ENTEROTOXIN (C-CPEM19); COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 3 ORGANISM_TAXID: 1502; SOURCE 4 GENE: CPE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN, CLAUDIN BINGER, C-CPE EXPDTA X-RAY DIFFRACTION AUTHOR H.AOYAMA REVDAT 1 18-JUN-25 9J7X 0 JRNL AUTH H.AOYAMA JRNL TITL CRYSTAL STRUCTURE OF QUINTUPLE MUTANT C TERMINAL FRAGMENT OF JRNL TITL 2 CLOSTRIDIUM PERFRINGENS ENTEROTOXIN (C-CPEM19) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21_5207: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 19432 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 987 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.8300 - 3.8200 0.96 2661 127 0.1544 0.1734 REMARK 3 2 3.8200 - 3.0300 1.00 2672 134 0.1975 0.2660 REMARK 3 3 3.0300 - 2.6500 1.00 2641 148 0.2367 0.2838 REMARK 3 4 2.6500 - 2.4100 1.00 2637 140 0.2339 0.2854 REMARK 3 5 2.4100 - 2.2300 1.00 2613 158 0.2382 0.2761 REMARK 3 6 2.2300 - 2.1000 1.00 2625 132 0.2329 0.2447 REMARK 3 7 2.1000 - 2.0000 1.00 2596 148 0.2938 0.3110 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 1010 REMARK 3 ANGLE : 1.144 1380 REMARK 3 CHIRALITY : 0.076 151 REMARK 3 PLANARITY : 0.009 178 REMARK 3 DIHEDRAL : 17.015 364 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9J7X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300050506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19458 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 63.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 10.90 REMARK 200 R MERGE FOR SHELL (I) : 0.90300 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MIXING 1 ML OF PROTEIN SOLUTION AT 9 REMARK 280 MG/ML, 1 ML OF RESERVOIR SOLUTION CONTAINING 0.1 M SODIUM REMARK 280 ACETATE PH 4.6 AND 1.75 M AMMONIUM SULFATE, AND ALLOWING THE REMARK 280 DROP TO EQUILIBRATE AGAINST 1 ML OF RESERVOIR SOLUTION BY THE REMARK 280 HANGING DROP METHOD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.27000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.54000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 42.54000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.27000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 443 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 449 LIES ON A SPECIAL POSITION. 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 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 SER A 181 REMARK 465 SER A 182 REMARK 465 GLY A 183 REMARK 465 HIS A 184 REMARK 465 ILE A 185 REMARK 465 GLU A 186 REMARK 465 PHE A 187 REMARK 465 ARG A 188 REMARK 465 HIS A 189 REMARK 465 MET A 190 REMARK 465 ASP A 191 REMARK 465 ILE A 192 REMARK 465 GLU A 193 REMARK 465 LYS A 194 REMARK 465 GLU A 195 REMARK 465 ILE A 196 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 LEU A 197 CG CD1 CD2 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 266 26.00 -144.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 9J7X A 191 319 UNP P01558 ELTB_CLOPF 194 319 SEQADV 9J7X HIS A 171 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 172 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 173 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 174 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 175 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 176 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 177 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 178 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 179 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 180 UNP P01558 EXPRESSION TAG SEQADV 9J7X SER A 181 UNP P01558 EXPRESSION TAG SEQADV 9J7X SER A 182 UNP P01558 EXPRESSION TAG SEQADV 9J7X GLY A 183 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 184 UNP P01558 EXPRESSION TAG SEQADV 9J7X ILE A 185 UNP P01558 EXPRESSION TAG SEQADV 9J7X GLU A 186 UNP P01558 EXPRESSION TAG SEQADV 9J7X PHE A 187 UNP P01558 EXPRESSION TAG SEQADV 9J7X ARG A 188 UNP P01558 EXPRESSION TAG SEQADV 9J7X HIS A 189 UNP P01558 EXPRESSION TAG SEQADV 9J7X MET A 190 UNP P01558 EXPRESSION TAG SEQADV 9J7X ALA A 304 UNP P01558 SER 304 ENGINEERED MUTATION SEQADV 9J7X PRO A 305 UNP P01558 SER 305 ENGINEERED MUTATION SEQADV 9J7X ARG A 307 UNP P01558 SER 307 ENGINEERED MUTATION SEQADV 9J7X HIS A 309 UNP P01558 ASN 309 ENGINEERED MUTATION SEQADV 9J7X HIS A 313 UNP P01558 SER 313 ENGINEERED MUTATION SEQRES 1 A 146 HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 146 HIS ILE GLU PHE ARG HIS MET ASP ILE GLU LYS GLU ILE SEQRES 3 A 146 LEU ASP LEU ALA ALA ALA THR GLU ARG LEU ASN LEU THR SEQRES 4 A 146 ASP ALA LEU ASN SER ASN PRO ALA GLY ASN LEU TYR ASP SEQRES 5 A 146 TRP ARG SER SER ASN SER TYR PRO TRP THR GLN LYS LEU SEQRES 6 A 146 ASN LEU HIS LEU THR ILE THR ALA THR GLY GLN LYS TYR SEQRES 7 A 146 ARG ILE LEU ALA SER LYS ILE VAL ASP PHE ASN ILE TYR SEQRES 8 A 146 SER ASN ASN PHE ASN ASN LEU VAL LYS LEU GLU GLN SER SEQRES 9 A 146 LEU GLY ASP GLY VAL LYS ASP HIS TYR VAL ASP ILE SER SEQRES 10 A 146 LEU ASP ALA GLY GLN TYR VAL LEU VAL MET LYS ALA ASN SEQRES 11 A 146 ALA PRO TYR ARG GLY HIS TYR PRO TYR HIS ILE LEU PHE SEQRES 12 A 146 GLN LYS PHE FORMUL 2 HOH *49(H2 O) HELIX 1 AA1 LEU A 208 SER A 217 1 7 HELIX 2 AA2 ASN A 267 ASN A 270 5 4 SHEET 1 AA1 5 ALA A 202 ASN A 207 0 SHEET 2 AA1 5 LEU A 238 ILE A 244 1 O HIS A 241 N GLU A 204 SHEET 3 AA1 5 GLY A 294 ALA A 302 -1 O LEU A 298 N LEU A 240 SHEET 4 AA1 5 VAL A 259 SER A 265 -1 N ASP A 260 O LYS A 301 SHEET 5 AA1 5 VAL A 272 SER A 277 -1 O SER A 277 N PHE A 261 SHEET 1 AA2 4 LEU A 223 ARG A 227 0 SHEET 2 AA2 4 HIS A 313 LYS A 318 -1 O PHE A 316 N TYR A 224 SHEET 3 AA2 4 GLN A 249 ALA A 255 -1 N ARG A 252 O GLN A 317 SHEET 4 AA2 4 HIS A 285 LEU A 291 -1 O HIS A 285 N ALA A 255 CRYST1 87.590 87.590 63.810 90.00 90.00 120.00 P 31 2 1 6 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 0.011417 0.006592 0.000000 0.00000 SCALE2 0.000000 0.013183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015671 0.00000 MASTER 272 0 0 2 9 0 0 6 1014 1 0 12 END