HEADER ANTIVIRAL PROTEIN 20-MAY-22 7ZXB TITLE CRYSTAL STRUCTURE OF HUMAN STING IN COMPLEX WITH 3',3'-C-(2'DAMP-2'F, TITLE 2 2'DAMP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: STIMULATOR OF INTERFERON PROTEIN; COMPND 3 CHAIN: A; COMPND 4 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: STING, LOC340061, HCG_1782396; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS STING, ANTIVIRAL, ACTIVATOR, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KLIMA,M.SMOLA,E.BOURA REVDAT 1 29-NOV-23 7ZXB 0 JRNL AUTH M.KLIMA,M.SMOLA,E.BOURA JRNL TITL CRYSTAL STRUCTURE OF HUMAN STING IN COMPLEX WITH JRNL TITL 2 3',3'-C-(2'DAMP-2'F,2'DAMP) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 4804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 241 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 35.3600 - 4.3200 0.99 2681 145 0.1996 0.2251 REMARK 3 2 4.3200 - 3.4300 1.00 2702 135 0.2395 0.2946 REMARK 3 3 3.4300 - 3.0000 1.00 2699 147 0.3156 0.3683 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) : 0.209 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.802 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 71.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.30 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 1474 REMARK 3 ANGLE : 0.515 2006 REMARK 3 CHIRALITY : 0.041 220 REMARK 3 PLANARITY : 0.003 256 REMARK 3 DIHEDRAL : 12.923 553 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 7ZXB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292123175. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS XDSAPP 2.0 REMARK 200 DATA SCALING SOFTWARE : XDS XDSAPP 2.0 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4804 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 16.20 REMARK 200 R MERGE (I) : 0.16120 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 17.30 REMARK 200 R MERGE FOR SHELL (I) : 1.25600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.590 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 4KSY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM ACETATE, 20% (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 17.55750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.90150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.90150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.77875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.90150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.90150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.33625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.90150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.90150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 8.77875 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.90150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.90150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.33625 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 17.55750 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: 4210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ALA A 140 REMARK 465 PRO A 141 REMARK 465 ALA A 142 REMARK 465 GLU A 143 REMARK 465 ILE A 144 REMARK 465 SER A 145 REMARK 465 ALA A 146 REMARK 465 VAL A 147 REMARK 465 CYS A 148 REMARK 465 GLU A 149 REMARK 465 LYS A 150 REMARK 465 GLY A 151 REMARK 465 ASN A 152 REMARK 465 PHE A 153 REMARK 465 ASN A 187 REMARK 465 ASN A 188 REMARK 465 LEU A 189 REMARK 465 LEU A 190 REMARK 465 ARG A 191 REMARK 465 GLY A 192 REMARK 465 PRO A 317 REMARK 465 ALA A 318 REMARK 465 ASP A 319 REMARK 465 ASP A 320 REMARK 465 GLU A 339 REMARK 465 GLU A 340 REMARK 465 VAL A 341 REMARK 465 THR A 342 REMARK 465 VAL A 343 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 180 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 310 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 338 CG CD CE NZ DBREF1 7ZXB A 140 343 UNP A0A2R3XZB7_HUMAN DBREF2 7ZXB A A0A2R3XZB7 140 343 SEQRES 1 A 204 ALA PRO ALA GLU ILE SER ALA VAL CYS GLU LYS GLY ASN SEQRES 2 A 204 PHE ASN VAL ALA HIS GLY LEU ALA TRP SER TYR TYR ILE SEQRES 3 A 204 GLY TYR LEU ARG LEU ILE LEU PRO GLU LEU GLN ALA ARG SEQRES 4 A 204 ILE ARG THR TYR ASN GLN HIS TYR ASN ASN LEU LEU ARG SEQRES 5 A 204 GLY ALA VAL SER GLN ARG LEU TYR ILE LEU LEU PRO LEU SEQRES 6 A 204 ASP CYS GLY VAL PRO ASP ASN LEU SER MET ALA ASP PRO SEQRES 7 A 204 ASN ILE ARG PHE LEU ASP LYS LEU PRO GLN GLN THR GLY SEQRES 8 A 204 ASP ARG ALA GLY ILE LYS ASP ARG VAL TYR SER ASN SER SEQRES 9 A 204 ILE TYR GLU LEU LEU GLU ASN GLY GLN ARG ALA GLY THR SEQRES 10 A 204 CYS VAL LEU GLU TYR ALA THR PRO LEU GLN THR LEU PHE SEQRES 11 A 204 ALA MET SER GLN TYR SER GLN ALA GLY PHE SER ARG GLU SEQRES 12 A 204 ASP ARG LEU GLU GLN ALA LYS LEU PHE CYS ARG THR LEU SEQRES 13 A 204 GLU ASP ILE LEU ALA ASP ALA PRO GLU SER GLN ASN ASN SEQRES 14 A 204 CYS ARG LEU ILE ALA TYR GLN GLU PRO ALA ASP ASP SER SEQRES 15 A 204 SER PHE SER LEU SER GLN GLU VAL LEU ARG HIS LEU ARG SEQRES 16 A 204 GLN GLU GLU LYS GLU GLU VAL THR VAL HET KAX A 401 43 HETNAM KAX 9-[(1~{R},6~{R},8~{R},10~{S},15~{R},17~{R},18~{S})-8- HETNAM 2 KAX (6-AMINOPURIN-9-YL)-18-FLUORANYL-3,12-BIS(OXIDANYL)-3, HETNAM 3 KAX 12-BIS(OXIDANYLIDENE)-2,4,7,11,13-PENTAOXA-3$L^{5}, HETNAM 4 KAX 12$L^{5}-DIPHOSPHATRICYCLO[13.3.0.0^{6,10}]OCTADECAN- HETNAM 5 KAX 17-YL]PURIN-6-AMINE FORMUL 2 KAX C21 H25 F N10 O9 P2 HELIX 1 AA1 VAL A 155 TYR A 167 1 13 HELIX 2 AA2 TYR A 167 TYR A 186 1 20 HELIX 3 AA3 ASN A 211 ASP A 216 1 6 HELIX 4 AA4 ALA A 262 SER A 272 1 11 HELIX 5 AA5 SER A 280 GLU A 282 5 3 HELIX 6 AA6 ASP A 283 ALA A 302 1 20 HELIX 7 AA7 SER A 324 GLU A 337 1 14 SHEET 1 AA1 5 ILE A 219 LYS A 224 0 SHEET 2 AA1 5 SER A 243 GLU A 249 -1 O GLU A 246 N ARG A 220 SHEET 3 AA1 5 GLN A 252 TYR A 261 -1 O CYS A 257 N TYR A 245 SHEET 4 AA1 5 LEU A 198 PRO A 203 1 N LEU A 201 O GLU A 260 SHEET 5 AA1 5 CYS A 309 TYR A 314 1 O ILE A 312 N LEU A 202 SHEET 1 AA2 2 GLN A 228 ARG A 232 0 SHEET 2 AA2 2 ILE A 235 TYR A 240 -1 O TYR A 240 N GLN A 228 CRYST1 111.803 111.803 35.115 90.00 90.00 90.00 P 41 21 2 8 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 0.008944 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028478 0.00000