HEADER TRANSFERASE 26-JAN-22 7WR2 TITLE CRYATAL STRUCTURE OF OSPC3 C-TERMINAL ANKYRIN-REPEAT DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: OSPC3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI; SOURCE 3 ORGANISM_TAXID: 623; SOURCE 4 GENE: OSPC3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-2 KEYWDS ADP-RIBOXANASE, EFFECTOR, ANKYRIN-REPEAT DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.HOU,H.ZENG,F.SHAO,J.DING REVDAT 4 29-NOV-23 7WR2 1 REMARK REVDAT 3 29-MAR-23 7WR2 1 JRNL REVDAT 2 01-FEB-23 7WR2 1 JRNL REVDAT 1 25-JAN-23 7WR2 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. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 19047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1905 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 40.0900 - 3.7200 0.99 1342 149 0.1609 0.1667 REMARK 3 2 3.7200 - 2.9500 0.99 1263 141 0.1657 0.1608 REMARK 3 3 2.9500 - 2.5800 0.99 1239 138 0.1718 0.2168 REMARK 3 4 2.5800 - 2.3400 1.00 1244 137 0.1734 0.1811 REMARK 3 5 2.3400 - 2.1800 0.99 1222 137 0.1628 0.1918 REMARK 3 6 2.1700 - 2.0500 0.99 1228 136 0.1634 0.2028 REMARK 3 7 2.0500 - 1.9400 0.99 1217 136 0.1673 0.2114 REMARK 3 8 1.9400 - 1.8600 0.99 1222 135 0.1796 0.2376 REMARK 3 9 1.8600 - 1.7900 0.99 1209 134 0.1754 0.1997 REMARK 3 10 1.7900 - 1.7300 0.99 1223 136 0.1851 0.2287 REMARK 3 11 1.7300 - 1.6700 0.99 1208 135 0.1750 0.2280 REMARK 3 12 1.6700 - 1.6200 0.99 1193 132 0.1800 0.1851 REMARK 3 13 1.6200 - 1.5800 0.99 1208 134 0.1713 0.2248 REMARK 3 14 1.5800 - 1.5400 0.92 1124 125 0.1789 0.2282 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) : 0.132 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.013 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.83 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 : 0.006 1107 REMARK 3 ANGLE : 0.837 1481 REMARK 3 CHIRALITY : 0.047 163 REMARK 3 PLANARITY : 0.004 189 REMARK 3 DIHEDRAL : 16.199 428 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 7WR2 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_1300027096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-18 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) : 0.97892 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 : 19087 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 40.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.020 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.15800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.870 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: 7WR1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG MONOMETHYL ETHER 550, 0.1 M REMARK 280 BIS-TRIS PROPANE PH 9.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.60750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.96600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.97150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.96600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.60750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.97150 REMARK 290 SMTRY3 4 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 GLY A 324 REMARK 465 PRO A 325 REMARK 465 LEU A 326 REMARK 465 GLY A 327 REMARK 465 SER A 328 REMARK 465 GLY A 329 REMARK 465 ARG A 330 REMARK 465 PRO A 331 REMARK 465 MET A 332 REMARK 465 LEU A 333 REMARK 465 SER A 334 REMARK 465 THR A 335 REMARK 465 ASP A 336 REMARK 465 ASN A 337 REMARK 465 PHE A 338 REMARK 465 LYS A 339 REMARK 465 LYS A 340 REMARK 465 ILE A 341 REMARK 465 LYS A 342 REMARK 465 LEU A 343 REMARK 465 ARG A 344 REMARK 465 ASP A 345 REMARK 465 PHE A 482 REMARK 465 GLU A 483 REMARK 465 ILE A 484 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 350 O HOH A 501 1.82 REMARK 500 O HOH A 621 O HOH A 633 1.86 REMARK 500 O HOH A 624 O HOH A 673 1.93 REMARK 500 NZ LYS A 473 O HOH A 502 2.05 REMARK 500 O HOH A 621 O HOH A 664 2.06 REMARK 500 O HOH A 506 O HOH A 649 2.07 REMARK 500 N ILE A 346 O HOH A 503 2.08 REMARK 500 O HOH A 586 O HOH A 652 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 636 O HOH A 664 3444 2.14 REMARK 500 O HOH A 613 O HOH A 638 2455 2.15 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 LYS A 382 74.69 -104.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 7WR2 A 332 484 UNP R4X5L7 R4X5L7_SHIFL 332 484 SEQADV 7WR2 GLY A 324 UNP R4X5L7 EXPRESSION TAG SEQADV 7WR2 PRO A 325 UNP R4X5L7 EXPRESSION TAG SEQADV 7WR2 LEU A 326 UNP R4X5L7 EXPRESSION TAG SEQADV 7WR2 GLY A 327 UNP R4X5L7 EXPRESSION TAG SEQADV 7WR2 SER A 328 UNP R4X5L7 EXPRESSION TAG SEQADV 7WR2 GLY A 329 UNP R4X5L7 EXPRESSION TAG SEQADV 7WR2 ARG A 330 UNP R4X5L7 EXPRESSION TAG SEQADV 7WR2 PRO A 331 UNP R4X5L7 EXPRESSION TAG SEQRES 1 A 161 GLY PRO LEU GLY SER GLY ARG PRO MET LEU SER THR ASP SEQRES 2 A 161 ASN PHE LYS LYS ILE LYS LEU ARG ASP ILE SER LEU GLU SEQRES 3 A 161 ASP ALA ILE LYS ALA SER ASN TYR GLU GLU ILE ASN ASN SEQRES 4 A 161 LYS VAL THR ASP LYS LYS MET ALA HIS GLN ALA LEU ALA SEQRES 5 A 161 TYR SER LEU GLY ASN LYS LYS ALA ASP ILE ALA LEU TYR SEQRES 6 A 161 LEU LEU SER LYS PHE ASN PHE THR LYS GLN ASP VAL ALA SEQRES 7 A 161 GLU MET GLU LYS MET LYS ASN ASN ARG TYR CYS ASN LEU SEQRES 8 A 161 TYR ASP VAL GLU TYR LEU LEU SER LYS ASP GLY ALA ASN SEQRES 9 A 161 TYR LYS VAL LEU GLU TYR PHE ILE ASN ASN GLY LEU VAL SEQRES 10 A 161 ASP VAL ASN LYS LYS PHE GLN LYS VAL ASN SER GLY ASP SEQRES 11 A 161 THR MET LEU ASP ASN ALA MET LYS SER LYS ASP SER LYS SEQRES 12 A 161 MET ILE ASP PHE LEU LEU LYS ASN GLY ALA ILE LEU GLY SEQRES 13 A 161 LYS ARG PHE GLU ILE FORMUL 2 HOH *176(H2 O) HELIX 1 AA1 SER A 347 ALA A 354 1 8 HELIX 2 AA2 ASN A 356 VAL A 364 1 9 HELIX 3 AA3 ASP A 366 ASN A 380 1 15 HELIX 4 AA4 LYS A 382 PHE A 393 1 12 HELIX 5 AA5 THR A 396 GLU A 404 1 9 HELIX 6 AA6 ASN A 409 TYR A 415 1 7 HELIX 7 AA7 ASP A 416 LYS A 423 1 8 HELIX 8 AA8 ASP A 424 ALA A 426 5 3 HELIX 9 AA9 ASN A 427 ASN A 437 1 11 HELIX 10 AB1 THR A 454 LYS A 463 1 10 HELIX 11 AB2 ASP A 464 ASN A 474 1 11 CRYST1 39.215 53.943 59.932 90.00 90.00 90.00 P 21 21 21 4 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 0.025500 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018538 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016686 0.00000