HEADER HYDROLASE 26-JAN-22 7WR0 TITLE P32 OF CASPASE-4 C258A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CASP-4; COMPND 5 EC: 3.4.22.57; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CASP4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A-SUMO KEYWDS PROTEASE, MUTANT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.HOU,H.ZENG,F.SHAO,J.DING REVDAT 4 29-NOV-23 7WR0 1 REMARK REVDAT 3 29-MAR-23 7WR0 1 JRNL REVDAT 2 01-FEB-23 7WR0 1 JRNL REVDAT 1 25-JAN-23 7WR0 0 JRNL AUTH Y.HOU,H.ZENG,Z.LI,N.FENG,F.MENG,Y.XU,L.LI,F.SHAO,J.DING JRNL TITL STRUCTURAL MECHANISMS OF CALMODULIN ACTIVATION OF SHIGELLA JRNL TITL 2 EFFECTOR OSPC3 TO ADP-RIBOXANATE CASPASE-4/11 AND BLOCK JRNL TITL 3 PYROPTOSIS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 261 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 36624349 JRNL DOI 10.1038/S41594-022-00888-3 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7697 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 765 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 36.1600 - 4.7800 1.00 1453 162 0.1972 0.2222 REMARK 3 2 4.7700 - 3.8000 1.00 1402 153 0.2274 0.2585 REMARK 3 3 3.7900 - 3.3200 1.00 1361 150 0.2690 0.2872 REMARK 3 4 3.3100 - 3.0100 1.00 1363 152 0.3144 0.3308 REMARK 3 5 3.0100 - 2.8000 0.99 1353 148 0.3353 0.4146 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.472 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.761 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.66 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 : 0.002 1962 REMARK 3 ANGLE : 0.464 2649 REMARK 3 CHIRALITY : 0.041 294 REMARK 3 PLANARITY : 0.003 342 REMARK 3 DIHEDRAL : 22.144 740 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 7WR0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300027090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7706 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 18.72 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.89800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.660 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: 6KMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M POTASSIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 57.21333 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 28.60667 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 28.60667 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 57.21333 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 SER A 98 REMARK 465 GLY A 99 REMARK 465 ARG A 100 REMARK 465 PRO A 101 REMARK 465 SER A 102 REMARK 465 THR A 103 REMARK 465 ARG A 259 REMARK 465 GLY A 260 REMARK 465 ALA A 261 REMARK 465 ASN A 262 REMARK 465 ARG A 263 REMARK 465 GLY A 264 REMARK 465 GLU A 265 REMARK 465 LEU A 266 REMARK 465 TRP A 267 REMARK 465 VAL A 268 REMARK 465 ARG A 269 REMARK 465 ASP A 270 REMARK 465 SER A 271 REMARK 465 PRO A 272 REMARK 465 ALA A 273 REMARK 465 SER A 274 REMARK 465 LEU A 275 REMARK 465 GLU A 276 REMARK 465 VAL A 277 REMARK 465 ALA A 278 REMARK 465 SER A 279 REMARK 465 SER A 280 REMARK 465 GLN A 281 REMARK 465 SER A 282 REMARK 465 SER A 283 REMARK 465 GLU A 284 REMARK 465 ASN A 285 REMARK 465 LEU A 286 REMARK 465 GLU A 287 REMARK 465 GLU A 288 REMARK 465 ASP A 289 REMARK 465 ALA A 290 REMARK 465 VAL A 291 REMARK 465 TYR A 292 REMARK 465 LYS A 293 REMARK 465 THR A 294 REMARK 465 HIS A 295 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 112 NH2 ARG A 189 5545 2.16 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 209 -172.65 -173.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 7WR0 A 102 377 UNP P49662 CASP4_HUMAN 102 377 SEQADV 7WR0 SER A 98 UNP P49662 EXPRESSION TAG SEQADV 7WR0 GLY A 99 UNP P49662 EXPRESSION TAG SEQADV 7WR0 ARG A 100 UNP P49662 EXPRESSION TAG SEQADV 7WR0 PRO A 101 UNP P49662 EXPRESSION TAG SEQADV 7WR0 ALA A 258 UNP P49662 CYS 258 ENGINEERED MUTATION SEQRES 1 A 280 SER GLY ARG PRO SER THR ASP ALA LEU LYS LEU CYS PRO SEQRES 2 A 280 HIS GLU GLU PHE LEU ARG LEU CYS LYS GLU ARG ALA GLU SEQRES 3 A 280 GLU ILE TYR PRO ILE LYS GLU ARG ASN ASN ARG THR ARG SEQRES 4 A 280 LEU ALA LEU ILE ILE CYS ASN THR GLU PHE ASP HIS LEU SEQRES 5 A 280 PRO PRO ARG ASN GLY ALA ASP PHE ASP ILE THR GLY MET SEQRES 6 A 280 LYS GLU LEU LEU GLU GLY LEU ASP TYR SER VAL ASP VAL SEQRES 7 A 280 GLU GLU ASN LEU THR ALA ARG ASP MET GLU SER ALA LEU SEQRES 8 A 280 ARG ALA PHE ALA THR ARG PRO GLU HIS LYS SER SER ASP SEQRES 9 A 280 SER THR PHE LEU VAL LEU MET SER HIS GLY ILE LEU GLU SEQRES 10 A 280 GLY ILE CYS GLY THR VAL HIS ASP GLU LYS LYS PRO ASP SEQRES 11 A 280 VAL LEU LEU TYR ASP THR ILE PHE GLN ILE PHE ASN ASN SEQRES 12 A 280 ARG ASN CYS LEU SER LEU LYS ASP LYS PRO LYS VAL ILE SEQRES 13 A 280 ILE VAL GLN ALA ALA ARG GLY ALA ASN ARG GLY GLU LEU SEQRES 14 A 280 TRP VAL ARG ASP SER PRO ALA SER LEU GLU VAL ALA SER SEQRES 15 A 280 SER GLN SER SER GLU ASN LEU GLU GLU ASP ALA VAL TYR SEQRES 16 A 280 LYS THR HIS VAL GLU LYS ASP PHE ILE ALA PHE CYS SER SEQRES 17 A 280 SER THR PRO HIS ASN VAL SER TRP ARG ASP SER THR MET SEQRES 18 A 280 GLY SER ILE PHE ILE THR GLN LEU ILE THR CYS PHE GLN SEQRES 19 A 280 LYS TYR SER TRP CYS CYS HIS LEU GLU GLU VAL PHE ARG SEQRES 20 A 280 LYS VAL GLN GLN SER PHE GLU THR PRO ARG ALA LYS ALA SEQRES 21 A 280 GLN MET PRO THR ILE GLU ARG LEU SER MET THR ARG TYR SEQRES 22 A 280 PHE TYR LEU PHE PRO GLY ASN HELIX 1 AA1 PRO A 110 ARG A 121 1 12 HELIX 2 AA2 ALA A 122 ILE A 125 5 4 HELIX 3 AA3 ALA A 155 LEU A 169 1 15 HELIX 4 AA4 THR A 180 THR A 193 1 14 HELIX 5 AA5 ARG A 194 LYS A 198 5 5 HELIX 6 AA6 TYR A 231 ASN A 239 1 9 HELIX 7 AA7 PRO A 308 SER A 312 5 5 HELIX 8 AA8 SER A 320 SER A 334 1 15 HELIX 9 AA9 HIS A 338 PHE A 350 1 13 SHEET 1 AA1 6 SER A 172 GLU A 177 0 SHEET 2 AA1 6 LEU A 137 CYS A 142 1 N ILE A 140 O GLU A 176 SHEET 3 AA1 6 THR A 203 MET A 208 1 O VAL A 206 N ILE A 141 SHEET 4 AA1 6 LYS A 251 GLN A 256 1 O ILE A 254 N LEU A 205 SHEET 5 AA1 6 PHE A 300 SER A 305 1 O ILE A 301 N ILE A 253 SHEET 6 AA1 6 THR A 361 GLU A 363 -1 O THR A 361 N CYS A 304 SHEET 1 AA2 2 GLY A 215 CYS A 217 0 SHEET 2 AA2 2 VAL A 228 LEU A 230 -1 O LEU A 229 N ILE A 216 CRYST1 77.571 77.571 85.820 90.00 90.00 120.00 P 32 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 0.012891 0.007443 0.000000 0.00000 SCALE2 0.000000 0.014886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011652 0.00000