HEADER ANTIVIRAL PROTEIN 21-FEB-24 8YDN TITLE CRYSTAL STRUCTURE OF A STING FROM C. GIGAS IN COMPLEX WITH C-DI-GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: STIMULATOR OF INTERFERON GENES PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRASSOSTREA GIGAS; SOURCE 3 ORGANISM_COMMON: PACIFIC OYSTER; SOURCE 4 ORGANISM_TAXID: 29159; SOURCE 5 GENE: CGI_10003079; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(CODON PLUS); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS COMPLEX, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,F.YU REVDAT 1 03-SEP-25 8YDN 0 JRNL AUTH Y.ZHANG,F.YU JRNL TITL CRYSTAL STRUCTURE OF TM-STING C-TERMINAL DOMAIN FROM THE JRNL TITL 2 PACIFIC OYSTER CRASSOSTREA GIGAS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 17310 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) : 0.233 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 874 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 70.9900 - 3.7100 1.00 2913 121 0.1930 0.1946 REMARK 3 2 3.7100 - 2.9400 1.00 2780 122 0.2304 0.2669 REMARK 3 3 2.9400 - 2.5700 1.00 2718 150 0.2774 0.3356 REMARK 3 4 2.5700 - 2.3400 1.00 2678 162 0.2867 0.3273 REMARK 3 5 2.3400 - 2.1700 0.99 2662 170 0.2872 0.2976 REMARK 3 6 2.1700 - 2.0400 1.00 2685 149 0.2911 0.3576 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) : 0.306 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.312 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.06 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 : 0.012 1567 REMARK 3 ANGLE : 1.544 2123 REMARK 3 CHIRALITY : 0.071 234 REMARK 3 PLANARITY : 0.009 267 REMARK 3 DIHEDRAL : 14.290 215 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 8YDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300044694. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17362 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 70.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 25.00 REMARK 200 R MERGE (I) : 0.18710 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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 (%): 25.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 400, 0.1 M MES PH 6.5, 2.0 M REMARK 280 AMMONIUM SULFATE, PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 52.20000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 52.20000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.41000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.20500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.20000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.61500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.20000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.61500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.20000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.20500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 52.20000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 52.20000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.41000 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 52.20000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 52.20000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 48.41000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 52.20000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 72.61500 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 52.20000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 24.20500 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 52.20000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 24.20500 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 52.20000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 72.61500 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 52.20000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 52.20000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 48.41000 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18030 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 -1.000000 0.000000 0.000000 52.20000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 72.61500 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 ALA A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 ILE A 6 REMARK 465 GLY A 7 REMARK 465 ILE A 8 REMARK 465 LEU A 9 REMARK 465 SER A 10 REMARK 465 MET A 11 REMARK 465 PHE A 12 REMARK 465 SER A 13 REMARK 465 VAL A 14 REMARK 465 THR A 15 REMARK 465 CYS A 16 REMARK 465 LYS A 17 REMARK 465 SER A 18 REMARK 465 THR A 19 REMARK 465 ASP A 20 REMARK 465 ASN A 21 REMARK 465 ASN A 22 REMARK 465 PHE A 23 REMARK 465 TRP A 24 REMARK 465 LYS A 25 REMARK 465 SER A 26 REMARK 465 THR A 27 REMARK 465 PHE A 28 REMARK 465 THR A 29 REMARK 465 SER A 30 REMARK 465 ASN A 31 REMARK 465 ASN A 32 REMARK 465 VAL A 33 REMARK 465 ASN A 34 REMARK 465 LEU A 35 REMARK 465 PHE A 36 REMARK 465 GLY A 37 REMARK 465 ASP A 38 REMARK 465 GLU A 39 REMARK 465 LEU A 40 REMARK 465 SER A 41 REMARK 465 TYR A 42 REMARK 465 ASN A 43 REMARK 465 LEU A 44 REMARK 465 ILE A 45 REMARK 465 PHE A 46 REMARK 465 VAL A 47 REMARK 465 THR A 48 REMARK 465 LEU A 49 REMARK 465 GLY A 50 REMARK 465 ILE A 51 REMARK 465 ILE A 52 REMARK 465 ASP A 53 REMARK 465 ILE A 54 REMARK 465 TRP A 55 REMARK 465 VAL A 56 REMARK 465 GLY A 57 REMARK 465 GLU A 58 REMARK 465 MET A 59 REMARK 465 ILE A 60 REMARK 465 LYS A 61 REMARK 465 ARG A 62 REMARK 465 VAL A 63 REMARK 465 PHE A 64 REMARK 465 VAL A 65 REMARK 465 PHE A 66 REMARK 465 CYS A 67 REMARK 465 GLY A 68 REMARK 465 GLU A 69 REMARK 465 PHE A 70 REMARK 465 ARG A 71 REMARK 465 PHE A 72 REMARK 465 ILE A 73 REMARK 465 ASN A 74 REMARK 465 SER A 75 REMARK 465 ARG A 76 REMARK 465 TYR A 77 REMARK 465 ASP A 78 REMARK 465 GLY A 79 REMARK 465 ARG A 80 REMARK 465 ILE A 81 REMARK 465 SER A 82 REMARK 465 PHE A 83 REMARK 465 VAL A 84 REMARK 465 VAL A 85 REMARK 465 GLN A 86 REMARK 465 GLN A 87 REMARK 465 SER A 88 REMARK 465 PHE A 89 REMARK 465 CYS A 90 REMARK 465 THR A 91 REMARK 465 LYS A 92 REMARK 465 SER A 93 REMARK 465 ASN A 94 REMARK 465 ILE A 95 REMARK 465 PRO A 96 REMARK 465 PHE A 97 REMARK 465 LEU A 98 REMARK 465 THR A 99 REMARK 465 LEU A 100 REMARK 465 PRO A 101 REMARK 465 ILE A 102 REMARK 465 LEU A 103 REMARK 465 VAL A 104 REMARK 465 ALA A 105 REMARK 465 MET A 106 REMARK 465 LEU A 107 REMARK 465 THR A 108 REMARK 465 TYR A 109 REMARK 465 MET A 110 REMARK 465 ASN A 111 REMARK 465 LEU A 112 REMARK 465 HIS A 113 REMARK 465 GLY A 114 REMARK 465 ASP A 115 REMARK 465 GLY A 116 REMARK 465 MET A 117 REMARK 465 LEU A 118 REMARK 465 LEU A 119 REMARK 465 ASP A 120 REMARK 465 PRO A 121 REMARK 465 THR A 122 REMARK 465 LYS A 123 REMARK 465 SER A 124 REMARK 465 GLU A 125 REMARK 465 MET A 126 REMARK 465 SER A 127 REMARK 465 ARG A 128 REMARK 465 VAL A 129 REMARK 465 MET A 130 REMARK 465 LYS A 299 REMARK 465 PHE A 300 REMARK 465 GLY A 301 REMARK 465 ASP A 302 REMARK 465 GLY A 303 REMARK 465 GLU A 304 REMARK 465 MET A 326 REMARK 465 VAL A 327 REMARK 465 ASP A 328 REMARK 465 ASP A 329 REMARK 465 PHE A 330 REMARK 465 ALA A 331 REMARK 465 LYS A 332 REMARK 465 VAL A 333 REMARK 465 VAL A 334 REMARK 465 ASP A 335 REMARK 465 GLY A 336 REMARK 465 THR A 337 REMARK 465 ASN A 338 REMARK 465 THR A 339 REMARK 465 ASP A 340 REMARK 465 THR A 341 REMARK 465 ILE A 342 REMARK 465 SER A 343 REMARK 465 SER A 344 REMARK 465 LYS A 345 REMARK 465 CYS A 346 REMARK 465 ALA A 347 REMARK 465 ASN A 348 REMARK 465 GLU A 349 REMARK 465 LEU A 350 REMARK 465 THR A 351 REMARK 465 GLU A 352 REMARK 465 ASP A 353 REMARK 465 ILE A 354 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 THR A 195 CG2 REMARK 470 THR A 207 CG2 REMARK 470 THR A 225 CG2 REMARK 470 THR A 271 CG2 REMARK 470 GLU A 278 CD OE1 OE2 REMARK 470 THR A 286 CG2 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 NZ LYS A 179 OD2 ASP A 318 2.10 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 O5' C2E A 401 O5A C2E A 401 5555 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 290 CB CYS A 290 SG -0.123 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 TYR A 149 -62.67 -150.86 REMARK 500 SER A 255 -43.80 -139.68 REMARK 500 GLU A 256 -22.36 87.61 REMARK 500 SER A 262 30.30 -96.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 C2E A 401 DBREF 8YDN A 1 354 UNP K1QMA0 K1QMA0_CRAGI 1 354 SEQADV 8YDN ALA A 171 UNP K1QMA0 THR 171 CONFLICT SEQADV 8YDN LEU A 182 UNP K1QMA0 ILE 182 CONFLICT SEQADV 8YDN ILE A 201 UNP K1QMA0 LEU 201 CONFLICT SEQADV 8YDN ARG A 267 UNP K1QMA0 GLN 267 CONFLICT SEQRES 1 A 354 MET ALA LEU GLY THR ILE GLY ILE LEU SER MET PHE SER SEQRES 2 A 354 VAL THR CYS LYS SER THR ASP ASN ASN PHE TRP LYS SER SEQRES 3 A 354 THR PHE THR SER ASN ASN VAL ASN LEU PHE GLY ASP GLU SEQRES 4 A 354 LEU SER TYR ASN LEU ILE PHE VAL THR LEU GLY ILE ILE SEQRES 5 A 354 ASP ILE TRP VAL GLY GLU MET ILE LYS ARG VAL PHE VAL SEQRES 6 A 354 PHE CYS GLY GLU PHE ARG PHE ILE ASN SER ARG TYR ASP SEQRES 7 A 354 GLY ARG ILE SER PHE VAL VAL GLN GLN SER PHE CYS THR SEQRES 8 A 354 LYS SER ASN ILE PRO PHE LEU THR LEU PRO ILE LEU VAL SEQRES 9 A 354 ALA MET LEU THR TYR MET ASN LEU HIS GLY ASP GLY MET SEQRES 10 A 354 LEU LEU ASP PRO THR LYS SER GLU MET SER ARG VAL MET SEQRES 11 A 354 GLU GLU GLN LYS LEU ASN VAL GLY HIS GLY LEU ALA TRP SEQRES 12 A 354 SER TYR TYR PHE GLY TYR LEU ARG LEU ILE ILE PRO GLY SEQRES 13 A 354 LEU GLN SER ARG MET ASP SER TRP LYS LYS GLY ILE ASP SEQRES 14 A 354 THR ALA ARG LYS SER VAL VAL VAL PRO LYS LEU TYR LEU SEQRES 15 A 354 LEU ILE PRO LYS SER CYS TYR CYS PRO PRO SER ILE THR SEQRES 16 A 354 ALA ALA ASP PRO GLN ILE LYS VAL ALA GLY VAL THR PRO SEQRES 17 A 354 SER PHE VAL ALA ASN ARG ALA GLY ASN GLN ARG ARG GLU SEQRES 18 A 354 TYR LYS ASN THR VAL TYR CYS PHE GLU ALA ASP LYS THR SEQRES 19 A 354 ASP PHE TYR CYS LEU VAL GLU TYR ALA THR PRO ILE LEU SEQRES 20 A 354 SER LEU TYR GLU MET SER ASN SER GLU GLU ALA GLY LEU SEQRES 21 A 354 SER SER PHE ASP ARG LEU ARG GLN MET ARG THR PHE VAL SEQRES 22 A 354 ALA THR LEU GLN GLU ILE ILE ASN SER ASN PRO GLU THR SEQRES 23 A 354 LYS ASP ASN CYS SER LEU LEU VAL TYR ASP ASP LYS LYS SEQRES 24 A 354 PHE GLY ASP GLY GLU GLN SER ILE SER MET LEU ILE LYS SEQRES 25 A 354 ASP ARG ILE GLU LYS ASP LEU SER ASP LYS ALA LEU GLN SEQRES 26 A 354 MET VAL ASP ASP PHE ALA LYS VAL VAL ASP GLY THR ASN SEQRES 27 A 354 THR ASP THR ILE SER SER LYS CYS ALA ASN GLU LEU THR SEQRES 28 A 354 GLU ASP ILE HET C2E A 401 35 HETNAM C2E 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10, HETNAM 2 C2E 12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3, HETNAM 3 C2E 2-D:3',2'-J][1,3,7,9,2, HETNAM 4 C2E 8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO- HETNAM 5 C2E 1,9-DIHYDRO-6H-PURIN-6-ONE) HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 2 C2E C20 H24 N10 O14 P2 HELIX 1 AA1 GLU A 132 ASN A 136 5 5 HELIX 2 AA2 VAL A 137 TYR A 149 1 13 HELIX 3 AA3 TYR A 149 ILE A 154 1 6 HELIX 4 AA4 GLY A 156 LYS A 166 1 11 HELIX 5 AA5 SER A 193 ASP A 198 1 6 HELIX 6 AA6 PRO A 245 ASN A 254 1 10 HELIX 7 AA7 GLU A 257 SER A 261 5 5 HELIX 8 AA8 ASP A 264 ASN A 283 1 20 HELIX 9 AA9 SER A 306 GLN A 325 1 20 SHEET 1 AA1 5 LYS A 202 VAL A 206 0 SHEET 2 AA1 5 THR A 225 ALA A 231 -1 O CYS A 228 N LYS A 202 SHEET 3 AA1 5 THR A 234 TYR A 242 -1 O CYS A 238 N TYR A 227 SHEET 4 AA1 5 LYS A 173 PRO A 185 1 N LYS A 173 O ASP A 235 SHEET 5 AA1 5 CYS A 290 TYR A 295 1 O LEU A 293 N ILE A 184 SHEET 1 AA2 2 PHE A 210 ARG A 214 0 SHEET 2 AA2 2 GLN A 218 TYR A 222 -1 O TYR A 222 N PHE A 210 CRYST1 104.400 104.400 96.820 90.00 90.00 90.00 I 41 2 2 16 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 0.009579 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010328 0.00000 CONECT 3015 3016 CONECT 3016 3015 3017 3039 3040 CONECT 3017 3016 3018 3019 3041 CONECT 3018 3017 3023 CONECT 3019 3017 3020 3021 3042 CONECT 3020 3019 3035 CONECT 3021 3019 3022 3023 3043 CONECT 3022 3021 3044 CONECT 3023 3018 3021 3024 3045 CONECT 3024 3023 3025 3034 CONECT 3025 3024 3026 3046 CONECT 3026 3025 3027 CONECT 3027 3026 3028 3034 CONECT 3028 3027 3029 3030 CONECT 3029 3028 CONECT 3030 3028 3031 3047 CONECT 3031 3030 3032 3033 CONECT 3032 3031 3048 3049 CONECT 3033 3031 3034 CONECT 3034 3024 3027 3033 CONECT 3035 3020 3036 3037 3038 CONECT 3036 3035 CONECT 3037 3035 CONECT 3038 3035 CONECT 3039 3016 CONECT 3040 3016 CONECT 3041 3017 CONECT 3042 3019 CONECT 3043 3021 CONECT 3044 3022 CONECT 3045 3023 CONECT 3046 3025 CONECT 3047 3030 CONECT 3048 3032 CONECT 3049 3032 MASTER 509 0 1 9 7 0 0 6 1526 1 35 28 END