HEADER TOXIN 20-JUL-25 9VYD TITLE CRYSTAL STRUCTURE OF TOXIN-ANTITOXIN COMPLEX VP14460-VP14465PEPTIDE TITLE 2 FROM VIBRIO PARAHAEMOLYTICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF1911 DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VP14460 (PONI); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VP14465 (PONE); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 670; SOURCE 4 GENE: TC_PAI_003; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS; SOURCE 9 ORGANISM_TAXID: 670; SOURCE 10 GENE: TC_PAI_002; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TYPE II TA SYSTEM, TOXIN-ANTITOXIN COMPLEX, MONOMER, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR F.HU REVDAT 1 22-JUL-26 9VYD 0 JRNL AUTH Y.ZHENG,C.ZHENG,Z.YE,L.HUANG,X.LIN,B.WU,Z.PAN,R.QIU,J.CAI, JRNL AUTH 2 L.XU,Z.DENG,R.XU,X.XIE,L.XIE,F.HU JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO THE VP14460-VP14465 JRNL TITL 2 EFFECTOR-IMMUNITY MODULE OF THE VIBRIO PARAHAEMOLYTICUS TYPE JRNL TITL 3 VI SECRETION SYSTEM. JRNL REF J.BIOL.CHEM. V. 302 13257 2026 JRNL REFN ESSN 1083-351X JRNL PMID 42297241 JRNL DOI 10.1016/J.JBC.2026.113257 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 3 NUMBER OF REFLECTIONS : 16196 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1619 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 6.9800 - 5.7200 0.99 1478 167 0.1927 0.2270 REMARK 3 2 5.7200 - 4.5400 0.98 1382 155 0.1969 0.2479 REMARK 3 3 4.5400 - 3.9700 0.98 1365 150 0.1870 0.2120 REMARK 3 4 3.9700 - 3.6100 0.96 1309 147 0.1997 0.2571 REMARK 3 5 3.6100 - 3.3500 0.92 1254 140 0.2401 0.2692 REMARK 3 6 3.3500 - 3.1500 0.94 1274 146 0.2228 0.2571 REMARK 3 7 3.1500 - 2.9900 0.89 1214 139 0.2443 0.2854 REMARK 3 8 2.9900 - 2.8600 0.85 1155 123 0.2437 0.2746 REMARK 3 9 2.8600 - 2.7500 0.85 1143 123 0.2814 0.3513 REMARK 3 10 2.7500 - 2.6600 0.76 1025 118 0.3190 0.4226 REMARK 3 11 2.6600 - 2.5700 0.72 974 99 0.3273 0.3574 REMARK 3 12 2.5700 - 2.5000 0.76 1004 112 0.3070 0.3826 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.600 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 : 0.003 2938 REMARK 3 ANGLE : 0.621 3981 REMARK 3 CHIRALITY : 0.041 417 REMARK 3 PLANARITY : 0.005 510 REMARK 3 DIHEDRAL : 4.760 378 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 9VYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 24-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061808. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-23 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL19U1 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 : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16207 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 57.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (1.0 M SODIUM CITRATE, 0.1 M CHES REMARK 280 PH9.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 53.66000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.54000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.54000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 80.49000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.54000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.54000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.83000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.54000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.54000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 80.49000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.54000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.54000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.83000 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 53.66000 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: 2110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 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 PRO A 221 97.40 -68.40 REMARK 500 GLU A 282 -5.62 70.39 REMARK 500 PRO A 309 -152.46 -84.89 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9VYD A 6 327 UNP A0A024B384_VIBPH DBREF2 9VYD A A0A024B384 1 322 DBREF1 9VYD B 1 23 UNP A0A024B2N9_VIBPH DBREF2 9VYD B A0A024B2N9 394 416 SEQADV 9VYD MET A 1 UNP A0A024B38 INITIATING METHIONINE SEQADV 9VYD ASN A 2 UNP A0A024B38 EXPRESSION TAG SEQADV 9VYD THR A 3 UNP A0A024B38 EXPRESSION TAG SEQADV 9VYD ASN A 4 UNP A0A024B38 EXPRESSION TAG SEQADV 9VYD GLU A 5 UNP A0A024B38 EXPRESSION TAG SEQRES 1 A 327 MET ASN THR ASN GLU MET LYS PHE THR GLN SER ARG ARG SEQRES 2 A 327 ASP PRO LEU LEU GLU LEU GLY VAL TYR GLU GLU VAL ASN SEQRES 3 A 327 ASN TYR PHE SER LYS ASP LYS THR PRO ARG PHE GLU LYS SEQRES 4 A 327 MET LYS ASP PRO THR LYS SER LEU THR ASN ARG SER ARG SEQRES 5 A 327 ILE SER TRP SER ILE THR LEU ASN CYS PHE GLU HIS ALA SEQRES 6 A 327 ILE LEU SER TYR SER GLY GLY GLN ALA MET GLU SER VAL SEQRES 7 A 327 LEU ASP LEU THR GLU VAL ALA LEU LYS ALA LEU GLU ARG SEQRES 8 A 327 HIS LYS ASN ASP PHE PRO HIS LYS SER TYR LEU PHE TRP SEQRES 9 A 327 GLU PRO ASP SER PHE GLN PHE LEU LEU TRP CYS LEU SER SEQRES 10 A 327 PHE VAL ALA LEU THR GLY LYS THR GLU TYR LEU SER THR SEQRES 11 A 327 ILE THR ARG MET TYR GLY THR SER PRO GLU VAL SER GLY SEQRES 12 A 327 GLU ALA CYS MET ALA GLN LEU PHE ARG LEU PHE ASN VAL SEQRES 13 A 327 HIS GLY ILE PRO ASP SER THR GLU GLU ALA LEU VAL PHE SEQRES 14 A 327 PRO ASP SER TYR GLN HIS LEU TYR ASN ALA ILE LYS THR SEQRES 15 A 327 GLY PRO LEU GLU PRO SER LYS LYS GLU ARG GLU GLU SER SEQRES 16 A 327 VAL LYS THR TYR LEU ARG GLY TRP TYR LYS GLY MET LYS SEQRES 17 A 327 ASP CYS TYR TRP HIS ASN ARG HIS LYS ALA ARG PHE PRO SEQRES 18 A 327 THR PHE PHE GLY TYR TRP ALA LEU GLU ALA ALA MET ILE SEQRES 19 A 327 THR LEU LEU PHE ASP LEU ASP ASP THR GLY TYR ASN HIS SEQRES 20 A 327 LEU PRO TYR TYR PRO LYS ASP TRP VAL ALA GLU ALA ARG SEQRES 21 A 327 LYS GLN GLY PHE ASP LYS LEU ILE LEU LYS ALA ASN LEU SEQRES 22 A 327 PRO SER ILE GLN VAL ALA PHE PRO GLU THR MET CYS PRO SEQRES 23 A 327 MET THR GLY GLU TRP GLN SER ASN LEU SER SER GLU VAL SEQRES 24 A 327 LEU SER LEU LYS GLU GLY GLU ILE MET PRO GLY PRO LEU SEQRES 25 A 327 GLN ASP GLU ASN GLU THR SER TYR PHE TRP VAL LEU GLN SEQRES 26 A 327 GLU ALA SEQRES 1 B 23 ASP GLY TRP ILE GLU PRO ARG LEU ILE ASP GLU LEU GLY SEQRES 2 B 23 LEU GLU GLY ALA GLU ASP ILE LEU ASP MET FORMUL 3 HOH *56(H2 O) HELIX 1 AA1 ASN A 2 ARG A 12 1 11 HELIX 2 AA2 GLU A 18 LYS A 31 1 14 HELIX 3 AA3 LYS A 33 LYS A 41 1 9 HELIX 4 AA4 SER A 46 GLY A 71 1 26 HELIX 5 AA5 ALA A 74 PHE A 96 1 23 HELIX 6 AA6 GLU A 105 GLY A 123 1 19 HELIX 7 AA7 LYS A 124 GLU A 126 5 3 HELIX 8 AA8 TYR A 127 MET A 134 1 8 HELIX 9 AA9 GLU A 144 PHE A 154 1 11 HELIX 10 AB1 PHE A 169 LYS A 181 1 13 HELIX 11 AB2 SER A 188 GLY A 202 1 15 HELIX 12 AB3 GLY A 202 MET A 207 1 6 HELIX 13 AB4 ASN A 214 ALA A 218 5 5 HELIX 14 AB5 ALA A 228 PHE A 238 1 11 HELIX 15 AB6 ASP A 241 TYR A 245 5 5 HELIX 16 AB7 PRO A 252 GLN A 262 1 11 HELIX 17 AB8 GLY A 263 ILE A 268 1 6 HELIX 18 AB9 ILE B 4 LEU B 21 1 18 SHEET 1 AA1 2 TYR A 101 LEU A 102 0 SHEET 2 AA1 2 TYR A 135 GLY A 136 1 O GLY A 136 N TYR A 101 SHEET 1 AA2 5 VAL A 156 HIS A 157 0 SHEET 2 AA2 5 ILE A 276 ALA A 279 1 O VAL A 278 N HIS A 157 SHEET 3 AA2 5 TRP A 322 GLN A 325 -1 O LEU A 324 N GLN A 277 SHEET 4 AA2 5 GLY A 289 SER A 293 -1 N GLN A 292 O VAL A 323 SHEET 5 AA2 5 VAL A 299 LEU A 302 -1 O LEU A 300 N TRP A 291 CRYST1 97.080 97.080 107.320 90.00 90.00 90.00 P 43 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 0.010301 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009318 0.00000 MASTER 239 0 0 18 7 0 0 6 2914 2 0 28 END