HEADER IMMUNE SYSTEM 19-JUN-24 9FRR TITLE CASPASE RECRUITMENT DOMAIN (CARD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE SERINE PROTEASE FE772_23065; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRYPSIN-LIKE PROTEASE 2; COMPND 5 EC: 3.4.21.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LYSOBACTER ENZYMOGENES; SOURCE 3 ORGANISM_TAXID: 69; SOURCE 4 GENE: FE772_23065, GA0399710_4915, GLE_4745; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CASPASE RECRUITMENT DOMAIN (CARD), IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR O.DYM,G.AMITAI,T.WEIN,R.SOREK REVDAT 2 12-FEB-25 9FRR 1 JRNL REVDAT 1 29-JAN-25 9FRR 0 JRNL AUTH T.WEIN,A.MILLMAN,K.LANGE,E.YIRMIYA,R.HADARY,J.GARB, JRNL AUTH 2 S.MELAMED,G.AMITAI,O.DYM,F.STEINRUECKE,A.B.HILL, JRNL AUTH 3 P.J.KRANZUSCH,R.SOREK JRNL TITL CARD DOMAINS MEDIATE ANTI-PHAGE DEFENCE IN BACTERIAL JRNL TITL 2 GASDERMIN SYSTEMS. JRNL REF NATURE 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 39880956 JRNL DOI 10.1038/S41586-024-08498-3 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15.2_3472: ???) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1564 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 17.5690 - 3.5495 1.00 2719 142 0.1535 0.1614 REMARK 3 2 3.5495 - 2.8211 1.00 2681 134 0.1897 0.2239 REMARK 3 3 2.8211 - 2.4656 1.00 2681 142 0.1977 0.2078 REMARK 3 4 2.4656 - 2.2407 1.00 2661 147 0.1839 0.2178 REMARK 3 5 2.2407 - 2.0804 1.00 2699 127 0.1749 0.1935 REMARK 3 6 2.0804 - 1.9579 1.00 2685 131 0.1920 0.2378 REMARK 3 7 1.9579 - 1.8599 1.00 2647 164 0.2073 0.2237 REMARK 3 8 1.8599 - 1.7791 1.00 2658 152 0.2032 0.2475 REMARK 3 9 1.7791 - 1.7106 1.00 2683 132 0.2033 0.2065 REMARK 3 10 1.7106 - 1.6516 1.00 2656 159 0.2086 0.2636 REMARK 3 11 1.6516 - 1.6000 1.00 2708 134 0.2115 0.2753 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.87 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 : 0.005 1498 REMARK 3 ANGLE : 0.658 2037 REMARK 3 CHIRALITY : 0.044 214 REMARK 3 PLANARITY : 0.004 269 REMARK 3 DIHEDRAL : 10.608 1189 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 9FRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292139547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.34 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-ARC 150 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31052 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 17.569 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 17.10 REMARK 200 R MERGE (I) : 0.06060 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.660 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9M SODIUM CITRATE TRIHYDRATE 0.05M REMARK 280 BIS-TRIS PROPANE PH=7, PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 81.40733 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 40.70367 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.05550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.35183 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 101.75917 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, B 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 1 REMARK 465 VAL A 2 REMARK 465 GLN A 3 REMARK 465 GLY A 95 REMARK 465 GLY B 95 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 ARG A 8 CZ NH1 NH2 REMARK 470 GLU A 39 CD OE1 OE2 REMARK 470 GLN A 90 CD OE1 NE2 REMARK 470 ASP A 93 CG OD1 OD2 REMARK 470 VAL B 2 CG1 CG2 REMARK 470 GLN B 3 CG CD OE1 NE2 REMARK 470 ARG B 8 CZ NH1 NH2 REMARK 470 GLN B 90 CD OE1 NE2 REMARK 470 ASP B 93 CG OD1 OD2 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 B 148 O HOH B 153 6554 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9FRR A 1 95 UNP PROT2_LYSEN DBREF2 9FRR A A0A0S2DN74 4 98 DBREF1 9FRR B 1 95 UNP PROT2_LYSEN DBREF2 9FRR B A0A0S2DN74 4 98 SEQADV 9FRR GLY A 1 UNP A0A0S2DN7 VAL 4 ENGINEERED MUTATION SEQADV 9FRR GLY B 1 UNP A0A0S2DN7 VAL 4 ENGINEERED MUTATION SEQRES 1 A 95 GLY VAL GLN ALA ASP TYR SER ARG ALA GLU ALA LEU ALA SEQRES 2 A 95 ALA TRP THR ARG LEU SER ASP GLU PHE ILE GLY ASN CYS SEQRES 3 A 95 TYR VAL SER VAL ARG PRO ARG HIS ALA PRO ALA TRP GLU SEQRES 4 A 95 VAL VAL VAL ALA SER ALA ALA GLY SER LEU ARG LEU GLU SEQRES 5 A 95 ALA PHE LYS ARG ALA HIS ASP HIS ASP PHE LEU ASP ARG SEQRES 6 A 95 LEU ALA VAL ALA ILE GLY ASN TRP GLU GLN LYS ALA GLN SEQRES 7 A 95 ARG PRO ASP HIS GLU ILE ALA GLN MET LEU ASP GLN VAL SEQRES 8 A 95 GLY ASP TYR GLY SEQRES 1 B 95 GLY VAL GLN ALA ASP TYR SER ARG ALA GLU ALA LEU ALA SEQRES 2 B 95 ALA TRP THR ARG LEU SER ASP GLU PHE ILE GLY ASN CYS SEQRES 3 B 95 TYR VAL SER VAL ARG PRO ARG HIS ALA PRO ALA TRP GLU SEQRES 4 B 95 VAL VAL VAL ALA SER ALA ALA GLY SER LEU ARG LEU GLU SEQRES 5 B 95 ALA PHE LYS ARG ALA HIS ASP HIS ASP PHE LEU ASP ARG SEQRES 6 B 95 LEU ALA VAL ALA ILE GLY ASN TRP GLU GLN LYS ALA GLN SEQRES 7 B 95 ARG PRO ASP HIS GLU ILE ALA GLN MET LEU ASP GLN VAL SEQRES 8 B 95 GLY ASP TYR GLY FORMUL 3 HOH *168(H2 O) HELIX 1 AA1 TYR A 6 THR A 16 1 11 HELIX 2 AA2 SER A 19 ARG A 31 1 13 HELIX 3 AA3 ALA A 37 ALA A 45 1 9 HELIX 4 AA4 SER A 48 HIS A 60 1 13 HELIX 5 AA5 PHE A 62 ALA A 77 1 16 HELIX 6 AA6 PRO A 80 GLY A 92 1 13 HELIX 7 AA7 TYR B 6 ALA B 14 1 9 HELIX 8 AA8 SER B 19 ARG B 31 1 13 HELIX 9 AA9 ALA B 37 ALA B 45 1 9 HELIX 10 AB1 SER B 48 HIS B 60 1 13 HELIX 11 AB2 PHE B 62 ALA B 77 1 16 HELIX 12 AB3 PRO B 80 GLY B 92 1 13 CRYST1 58.414 58.414 122.111 90.00 90.00 120.00 P 65 12 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 0.017119 0.009884 0.000000 0.00000 SCALE2 0.000000 0.019768 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008189 0.00000