HEADER TRANSFERASE 06-SEP-25 9WOO TITLE VCCDNG,A CD-NTASE FROM VIBRIO CHOLERAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC GMP-AMP SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: GENBANK AKB05927.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE 365-96; SOURCE 3 ORGANISM_TAXID: 1290432; SOURCE 4 STRAIN: 10432-62; SOURCE 5 GENE: EYB64_17215; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CBASS, CD-NTASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.YE REVDAT 1 09-SEP-26 9WOO 0 JRNL AUTH F.YE,J.GONG,Y.GE,Z.LI,S.YIN,A.GAO,Y.ZHU JRNL TITL DYNAMIC CONTROL OF BACTERIAL ANTIPHAGE DEFENSE THROUGH THE JRNL TITL 2 CDNG-CAP5 CYCLIC OLIGONUCLEOTIDE-BASED ANTIPHAGE PATHWAY IN JRNL TITL 3 VIBRIO CHOLERAE. JRNL REF J.BIOL.CHEM. V. 302 11021 2026 JRNL REFN ESSN 1083-351X JRNL PMID 41360261 JRNL DOI 10.1016/J.JBC.2025.111021 REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1-4487-000) 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) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 30087 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1465 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 19.8600 - 5.2900 0.93 2788 130 0.1802 0.1970 REMARK 3 2 5.2900 - 4.2100 0.96 2815 155 0.1569 0.1897 REMARK 3 3 4.2100 - 3.6800 0.97 2850 154 0.1699 0.2175 REMARK 3 4 3.6800 - 3.3500 0.97 2861 133 0.1931 0.2207 REMARK 3 5 3.3500 - 3.1100 0.98 2849 160 0.2335 0.2663 REMARK 3 6 3.1100 - 2.9300 0.99 2895 146 0.2444 0.2771 REMARK 3 7 2.9300 - 2.7800 0.99 2852 142 0.2440 0.2631 REMARK 3 8 2.7800 - 2.6600 0.99 2925 139 0.2715 0.3412 REMARK 3 9 2.6600 - 2.5600 1.00 2909 158 0.2712 0.2926 REMARK 3 10 2.5600 - 2.4700 1.00 2878 148 0.3006 0.3044 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.770 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 : 0.002 3206 REMARK 3 ANGLE : 0.418 4335 REMARK 3 CHIRALITY : 0.035 471 REMARK 3 PLANARITY : 0.003 563 REMARK 3 DIHEDRAL : 3.840 426 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 9WOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 09-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300063473. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-21 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 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 : 30871 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 19.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 74.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES,SODIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289.15K 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 54.41800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.05600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.41800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 59.05600 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 GLU A 69 REMARK 465 GLN A 386 REMARK 465 SER A 387 REMARK 465 SER A 388 REMARK 465 GLN A 396 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 GLU A 28 CG CD OE1 OE2 REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 GLU A 162 CG CD OE1 OE2 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 GLN A 71 -155.39 -122.75 REMARK 500 ALA A 127 -6.14 -142.44 REMARK 500 ASN A 194 70.06 -152.59 REMARK 500 ASN A 254 51.22 -157.14 REMARK 500 ASN A 305 81.44 -164.33 REMARK 500 CYS A 343 -71.67 -99.47 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9WOO A 1 396 UNP A0A7Z7VLQ0_VIBCL DBREF2 9WOO A A0A7Z7VLQ0 1 396 SEQADV 9WOO ILE A 98 UNP A0A7Z7VLQ VAL 98 CONFLICT SEQADV 9WOO ASP A 187 UNP A0A7Z7VLQ ASN 187 CONFLICT SEQRES 1 A 396 MET SER ASN SER LYS SER ASN ASP VAL LEU ASN THR ILE SEQRES 2 A 396 LEU GLU LYS ILE GLU LEU PRO ASP SER ALA TYR GLU LYS SEQRES 3 A 396 ALA GLU LYS ARG TYR LYS ASP LEU GLY ASP TRP LEU HIS SEQRES 4 A 396 ARG PRO GLU SER THR CYS VAL ASN PHE ASP PRO HIS VAL SEQRES 5 A 396 PHE SER GLN GLY SER PHE ARG LEU GLY THR ALA ILE ARG SEQRES 6 A 396 PRO ASP SER GLU GLU GLN TYR ASP LEU ASP MET GLY CYS SEQRES 7 A 396 ASN LEU ARG ARG GLY LEU ASP LYS THR SER ILE THR GLN SEQRES 8 A 396 LYS GLN LEU LYS HIS LEU ILE GLY HIS GLU LEU GLU LEU SEQRES 9 A 396 TYR ARG ASN ALA ARG GLY ILE LYS GLU GLU LEU ALA GLU SEQRES 10 A 396 LYS LYS ARG CYS TRP ARG LEU GLU TYR ALA ASP GLY LEU SEQRES 11 A 396 SER PHE HIS MET ASP ILE VAL PRO CYS VAL PRO GLU SER SEQRES 12 A 396 ASP THR GLY ARG GLY LEU LEU LYS LYS ARG MET VAL GLU SEQRES 13 A 396 ASN SER LYS PHE ASP GLU ASN LEU ALA GLN ASN VAL SER SEQRES 14 A 396 GLN LEU ALA VAL SER ILE THR ASP ASN THR ASP SER THR SEQRES 15 A 396 TYR ALA VAL VAL ASP GLU ASN TRP ARG ILE SER ASN PRO SEQRES 16 A 396 GLU GLY TYR ALA ARG TRP PHE GLU THR ARG MET LYS THR SEQRES 17 A 396 ALA ARG LEU VAL ILE ASN GLU ARG GLU MET ARG PHE LYS SEQRES 18 A 396 ALA SER ILE ASP SER LEU PRO TYR TYR GLN TRP LYS THR SEQRES 19 A 396 PRO LEU GLN GLN VAL ILE GLN LEU LEU LYS ARG HIS ARG SEQRES 20 A 396 ASP THR MET PHE LYS ASN ASN GLU ASP SER LYS PRO ILE SEQRES 21 A 396 SER VAL ILE ILE THR THR LEU ALA ALA LYS SER TYR LYS SEQRES 22 A 396 GLY GLU SER ASP LEU ALA SER ALA LEU ASN THR VAL LEU SEQRES 23 A 396 SER GLU MET ASP ASP HIS ILE SER ALA GLN ALA PRO MET SEQRES 24 A 396 ILE PRO ASN PRO VAL ASN PRO ALA GLU ASP PHE ALA ASP SEQRES 25 A 396 LYS TRP TYR ASP GLU LYS SER ALA GLN TYR ARG LEU GLN SEQRES 26 A 396 GLU ASN PHE TYR LYS TRP LEU TYR GLN ALA ARG ALA ASP SEQRES 27 A 396 PHE SER ALA LEU CYS SER SER ASP ASP THR GLN ARG ILE SEQRES 28 A 396 VAL ASN ALA ALA GLN ASN GLY LEU ASP LEU LYS LEU ASP SEQRES 29 A 396 SER SER SER VAL ALA ARG LEU LEU GLY ILE PRO ALA VAL SEQRES 30 A 396 THR ALA LYS PRO THR PHE ALA ILE GLN SER SER ASP PRO SEQRES 31 A 396 LYS PRO TRP PHE LYS GLN FORMUL 2 HOH *61(H2 O) HELIX 1 AA1 SER A 2 GLU A 18 1 17 HELIX 2 AA2 PRO A 20 ARG A 40 1 21 HELIX 3 AA3 CYS A 45 PHE A 48 5 4 HELIX 4 AA4 GLY A 56 GLY A 61 1 6 HELIX 5 AA5 THR A 90 GLY A 110 1 21 HELIX 6 AA6 SER A 143 ASN A 157 1 15 HELIX 7 AA7 ASP A 161 GLN A 170 1 10 HELIX 8 AA8 ASN A 194 LYS A 207 1 14 HELIX 9 AA9 ALA A 209 PHE A 220 1 12 HELIX 10 AB1 SER A 223 LEU A 227 5 5 HELIX 11 AB2 PRO A 228 TRP A 232 5 5 HELIX 12 AB3 THR A 234 PHE A 251 1 18 HELIX 13 AB4 ASN A 254 LYS A 258 5 5 HELIX 14 AB5 ILE A 260 TYR A 272 1 13 HELIX 15 AB6 ASP A 277 MET A 289 1 13 HELIX 16 AB7 ASP A 290 ILE A 293 5 4 HELIX 17 AB8 ALA A 311 TYR A 322 5 12 HELIX 18 AB9 ARG A 323 SER A 344 1 22 HELIX 19 AC1 ASP A 347 ASP A 360 1 14 HELIX 20 AC2 ASP A 364 LEU A 372 1 9 HELIX 21 AC3 PRO A 375 ALA A 379 5 5 SHEET 1 AA1 5 PRO A 50 GLN A 55 0 SHEET 2 AA1 5 TYR A 72 LEU A 80 -1 O ASN A 79 N HIS A 51 SHEET 3 AA1 5 PHE A 132 PRO A 141 1 O HIS A 133 N LEU A 74 SHEET 4 AA1 5 TRP A 122 TYR A 126 -1 N TRP A 122 O ILE A 136 SHEET 5 AA1 5 ALA A 116 GLU A 117 -1 N ALA A 116 O ARG A 123 SHEET 1 AA2 5 PRO A 50 GLN A 55 0 SHEET 2 AA2 5 TYR A 72 LEU A 80 -1 O ASN A 79 N HIS A 51 SHEET 3 AA2 5 PHE A 132 PRO A 141 1 O HIS A 133 N LEU A 74 SHEET 4 AA2 5 VAL A 173 ILE A 175 -1 O SER A 174 N VAL A 140 SHEET 5 AA2 5 ARG A 191 SER A 193 -1 O SER A 193 N VAL A 173 SHEET 1 AA3 2 PRO A 301 ASN A 302 0 SHEET 2 AA3 2 ASN A 305 ASP A 309 -1 O GLU A 308 N ASN A 302 CISPEP 1 ALA A 297 PRO A 298 0 1.18 CRYST1 108.836 118.112 78.071 90.00 119.49 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 0.009188 0.000000 0.005196 0.00000 SCALE2 0.000000 0.008467 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014715 0.00000 MASTER 240 0 0 21 12 0 0 6 3202 1 0 31 END