HEADER HYDROLASE 15-AUG-18 6AGW TITLE PRO-DOMAIN OF CASPASE-8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-8 PRO-DOMAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-180; COMPND 5 SYNONYM: CASP-8; COMPND 6 EC: 3.4.22.61; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CASP8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRO-DOMAIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.H.PARK REVDAT 2 27-MAR-24 6AGW 1 REMARK REVDAT 1 26-JUN-19 6AGW 0 JRNL AUTH H.H.PARK JRNL TITL MOLECULAR BASIS OF DIMERIZATION OF INITIATOR CASPASE WAS JRNL TITL 2 REVEALED BY CRYSTAL STRUCTURE OF CASPASE-8 PRO-DOMAIN. JRNL REF CELL DEATH DIFFER. V. 26 1213 2019 JRNL REFN ISSN 1350-9047 JRNL PMID 30206319 JRNL DOI 10.1038/S41418-018-0200-X REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 15183 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1504 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 29.6351 - 4.6484 0.92 1210 133 0.2062 0.2615 REMARK 3 2 4.6484 - 3.6918 0.94 1194 133 0.1950 0.2219 REMARK 3 3 3.6918 - 3.2258 0.98 1254 134 0.2175 0.2587 REMARK 3 4 3.2258 - 2.9311 1.00 1257 146 0.2434 0.2852 REMARK 3 5 2.9311 - 2.7212 1.00 1261 140 0.2364 0.3160 REMARK 3 6 2.7212 - 2.5609 1.00 1278 135 0.2401 0.2729 REMARK 3 7 2.5609 - 2.4327 1.00 1263 137 0.2377 0.3315 REMARK 3 8 2.4327 - 2.3268 1.00 1249 141 0.2381 0.2984 REMARK 3 9 2.3268 - 2.2373 1.00 1256 144 0.2307 0.2962 REMARK 3 10 2.2373 - 2.1601 1.00 1256 141 0.2449 0.3241 REMARK 3 11 2.1601 - 2.0926 0.95 1201 120 0.2554 0.2875 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.350 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 : 0.008 1512 REMARK 3 ANGLE : 1.047 2022 REMARK 3 CHIRALITY : 0.043 228 REMARK 3 PLANARITY : 0.004 260 REMARK 3 DIHEDRAL : 17.425 612 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 106.9627 -27.8246 17.3807 REMARK 3 T TENSOR REMARK 3 T11: 0.2559 T22: 0.2365 REMARK 3 T33: 0.2520 T12: -0.0220 REMARK 3 T13: 0.0140 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 1.1139 L22: 0.0716 REMARK 3 L33: 0.2366 L12: -0.1179 REMARK 3 L13: 0.6128 L23: 0.0306 REMARK 3 S TENSOR REMARK 3 S11: -0.0592 S12: 0.0688 S13: -0.0740 REMARK 3 S21: -0.0179 S22: 0.0953 S23: -0.0220 REMARK 3 S31: -0.1088 S32: 0.0231 S33: 0.0002 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 6AGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008749. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15189 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 (%): 58.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, CACODYLATE, NACL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.35850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.40350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.35850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.40350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL 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 246.53848 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.39699 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 MET A 1 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 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 O HOH A 220 O HOH A 243 2.14 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 OE1 GLU A 85 NH1 ARG A 88 2756 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 ARG A 33 103.35 -54.40 REMARK 500 GLU A 36 67.10 -117.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 244 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A 245 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH A 246 DISTANCE = 9.01 ANGSTROMS DBREF 6AGW A 1 180 UNP Q14790 CASP8_HUMAN 1 180 SEQADV 6AGW HIS A 181 UNP Q14790 EXPRESSION TAG SEQADV 6AGW HIS A 182 UNP Q14790 EXPRESSION TAG SEQADV 6AGW HIS A 183 UNP Q14790 EXPRESSION TAG SEQADV 6AGW HIS A 184 UNP Q14790 EXPRESSION TAG SEQADV 6AGW HIS A 185 UNP Q14790 EXPRESSION TAG SEQRES 1 A 185 MET ASP PHE SER ARG ASN LEU TYR ASP ILE GLY GLU GLN SEQRES 2 A 185 LEU ASP SER GLU ASP LEU ALA SER LEU LYS PHE LEU SER SEQRES 3 A 185 LEU ASP TYR ILE PRO GLN ARG LYS GLN GLU PRO ILE LYS SEQRES 4 A 185 ASP ALA LEU MET LEU PHE GLN ARG LEU GLN GLU LYS ARG SEQRES 5 A 185 MET LEU GLU GLU SER ASN LEU SER PHE LEU LYS GLU LEU SEQRES 6 A 185 LEU PHE ARG ILE ASN ARG LEU ASP LEU LEU ILE THR TYR SEQRES 7 A 185 LEU ASN THR ARG LYS GLU GLU MET GLU ARG GLU LEU GLN SEQRES 8 A 185 THR PRO GLY ARG ALA GLN ILE SER ALA TYR ARG VAL MET SEQRES 9 A 185 LEU TYR GLN ILE SER GLU GLU VAL SER ARG SER GLU LEU SEQRES 10 A 185 ARG SER PHE LYS PHE LEU LEU GLN GLU GLU ILE SER LYS SEQRES 11 A 185 CYS LYS LEU ASP ASP ASP MET ASN LEU LEU ASP ILE PHE SEQRES 12 A 185 ILE GLU MET GLU LYS ARG VAL ILE LEU GLY GLU GLY LYS SEQRES 13 A 185 LEU ASP ILE LEU LYS ARG VAL CYS ALA GLN ILE ASN LYS SEQRES 14 A 185 SER LEU LEU LYS ILE ILE ASN ASP TYR GLU GLU HIS HIS SEQRES 15 A 185 HIS HIS HIS FORMUL 2 HOH *46(H2 O) HELIX 1 AA1 ASP A 2 GLN A 13 1 12 HELIX 2 AA2 ASP A 15 SER A 26 1 12 HELIX 3 AA3 ASP A 40 LYS A 51 1 12 HELIX 4 AA4 LEU A 59 ILE A 69 1 11 HELIX 5 AA5 ARG A 71 ASN A 80 1 10 HELIX 6 AA6 ARG A 82 THR A 92 1 11 HELIX 7 AA7 SER A 99 VAL A 112 1 14 HELIX 8 AA8 SER A 113 LYS A 130 1 18 HELIX 9 AA9 ASN A 138 ARG A 149 1 12 HELIX 10 AB1 LEU A 157 GLN A 166 1 10 HELIX 11 AB2 ASN A 168 GLU A 179 1 12 CRYST1 90.717 62.807 52.997 90.00 118.90 90.00 C 1 2 1 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 0.011023 0.000000 0.006085 0.00000 SCALE2 0.000000 0.015922 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021553 0.00000