HEADER HYDROLASE 12-AUG-25 9WAU TITLE CRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM VIRULENCE PROTEIN CTEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CTEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHROMOBACTERIUM VIOLACEUM; SOURCE 3 ORGANISM_TAXID: 536; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS PAPAIN-LIKE PROTEASE, T3SS EFFECTORS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.SHAN,P.XING REVDAT 1 22-APR-26 9WAU 0 JRNL AUTH X.PAN,Y.ZHAO,J.LUO,L.DING,L.MA,Y.LI,J.XUE,X.TAO,S.OUYANG, JRNL AUTH 2 S.LI JRNL TITL PATHOGEN HIJACKS FOCAL ADHESION SIGNALING BY A T3SS EFFECTOR JRNL TITL 2 CTEX. JRNL REF PROC.NATL.ACAD.SCI.USA V. 123 73123 2026 JRNL REFN ESSN 1091-6490 JRNL PMID 41945428 JRNL DOI 10.1073/PNAS.2530673123 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 36525 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.370 REMARK 3 FREE R VALUE TEST SET COUNT : 1960 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 29.0500 - 3.6200 1.00 2717 150 0.1672 0.1916 REMARK 3 2 3.6200 - 2.8800 1.00 2581 151 0.1691 0.2114 REMARK 3 3 2.8800 - 2.5100 1.00 2574 146 0.1925 0.2578 REMARK 3 4 2.5100 - 2.2800 0.99 2514 138 0.1982 0.2206 REMARK 3 5 2.2800 - 2.1200 0.98 2481 145 0.1933 0.2497 REMARK 3 6 2.1200 - 2.0000 1.00 2542 134 0.1878 0.2426 REMARK 3 7 2.0000 - 1.9000 0.96 2401 140 0.2300 0.2610 REMARK 3 8 1.9000 - 1.8100 0.93 2320 145 0.2122 0.2643 REMARK 3 9 1.8100 - 1.7400 0.98 2474 131 0.1906 0.1965 REMARK 3 10 1.7400 - 1.6800 0.98 2442 142 0.1894 0.2449 REMARK 3 11 1.6800 - 1.6300 0.97 2428 133 0.1965 0.2683 REMARK 3 12 1.6300 - 1.5800 0.96 2422 138 0.2160 0.2729 REMARK 3 13 1.5800 - 1.5400 0.95 2360 138 0.2401 0.2656 REMARK 3 14 1.5400 - 1.5000 0.92 2309 129 0.2630 0.2804 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.110 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 : 0.014 1995 REMARK 3 ANGLE : 1.443 2696 REMARK 3 CHIRALITY : 0.074 290 REMARK 3 PLANARITY : 0.011 359 REMARK 3 DIHEDRAL : 15.401 742 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 9WAU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 19-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300062503. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37433 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.06913 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 (%): 36.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M AMMONIUM SULFATE, 0.1 M HEPES (PH REMARK 280 7.0), 0.8% (W/V) PEG 8000, AND 15% (V/V) GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.06950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.73050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.52050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.73050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.06950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.52050 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 MET A 91 REMARK 465 GLY A 92 REMARK 465 GLY A 93 REMARK 465 LEU A 94 REMARK 465 LEU A 95 REMARK 465 ARG A 184 REMARK 465 GLY A 185 REMARK 465 PRO A 186 REMARK 465 ARG A 187 REMARK 465 GLY A 188 REMARK 465 ASP A 189 REMARK 465 ALA A 190 REMARK 465 THR A 191 REMARK 465 HIS A 357 REMARK 465 HIS A 358 REMARK 465 HIS A 359 REMARK 465 HIS A 360 REMARK 465 HIS A 361 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 MET A 284 CG - SD - CE ANGL. DEV. = -14.9 DEGREES 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 VAL A 128 -51.11 -128.04 REMARK 500 ASN A 219 30.91 -151.43 REMARK 500 TYR A 298 -49.05 -135.86 REMARK 500 PRO A 335 -34.74 -39.59 REMARK 500 ASP A 349 -128.08 51.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 9WAU A 91 361 PDB 9WAU 9WAU 91 361 SEQRES 1 A 271 MET GLY GLY LEU LEU ASP ARG MET ARG MET LEU LEU ALA SEQRES 2 A 271 ASN PRO PHE GLU LYS THR LEU ASN ALA GLN GLY GLY ALA SEQRES 3 A 271 ASP GLN LYS LEU VAL PHE ASP GLN LYS LEU ALA VAL LEU SEQRES 4 A 271 THR PRO CYS ARG ALA ASP LEU ALA LYS LEU GLY LEU THR SEQRES 5 A 271 ASP MET LYS GLU GLY VAL CYS ASN GLY LEU SER TYR ALA SEQRES 6 A 271 TRP ALA GLU GLU GLN LEU LYS THR GLY ASN GLY ALA ASN SEQRES 7 A 271 THR LEU ASP TRP ILE ALA ARG VAL ALA ALA SER ASP SER SEQRES 8 A 271 LEU ALA ARG GLY PRO ARG GLY ASP ALA THR PRO SER ALA SEQRES 9 A 271 LEU SER GLN SER ARG ILE PRO LEU LEU ASN GLN LEU LYS SEQRES 10 A 271 LYS MET GLN ASP PHE GLN PHE SER GLN PHE ALA ASN THR SEQRES 11 A 271 GLY SER PRO LYS GLN ASP MET SER ASN TYR LEU GLN ALA SEQRES 12 A 271 VAL ASP GLY TRP GLY LYS ARG ASN GLY MET ASP ALA SER SEQRES 13 A 271 VAL ASP ILE LEU ASN PRO GLY ALA THR PRO ALA GLU ARG SEQRES 14 A 271 GLN LEU CYS ALA ARG LEU PRO ALA HIS ASP ASP GLY ALA SEQRES 15 A 271 LEU VAL PHE ARG THR THR GLU HIS THR MET ALA MET SER SEQRES 16 A 271 SER ARG GLY GLY THR TYR SER PHE PHE GLU PRO ASN TYR SEQRES 17 A 271 GLY MET ALA SER PHE GLN ASP LYS ARG ARG PHE ASP ASP SEQRES 18 A 271 PHE VAL ALA ALA PHE LEU LEU ALA GLU GLY HIS LYS PRO SEQRES 19 A 271 PRO PHE MET LEU THR GLU LEU LYS LEU ASP PRO GLY VAL SEQRES 20 A 271 PRO PRO ALA PRO THR ARG MET ALA GLU LEU ALA ASP ILE SEQRES 21 A 271 GLU LEU GLU HIS HIS HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *233(H2 O) HELIX 1 AA1 ASP A 96 LEU A 102 1 7 HELIX 2 AA2 ASN A 104 GLN A 113 1 10 HELIX 3 AA3 ASP A 123 VAL A 128 1 6 HELIX 4 AA4 CYS A 132 GLY A 140 1 9 HELIX 5 AA5 VAL A 148 GLY A 164 1 17 HELIX 6 AA6 ASN A 165 ALA A 178 1 14 HELIX 7 AA7 SER A 193 ASP A 211 1 19 HELIX 8 AA8 GLN A 213 ALA A 218 5 6 HELIX 9 AA9 SER A 222 ASN A 241 1 20 HELIX 10 AB1 PRO A 256 ARG A 264 1 9 HELIX 11 AB2 ASP A 305 GLY A 321 1 17 HELIX 12 AB3 THR A 342 ASP A 349 1 8 HELIX 13 AB4 ILE A 350 LEU A 352 5 3 SHEET 1 AA1 7 GLN A 118 VAL A 121 0 SHEET 2 AA1 7 GLY A 299 PHE A 303 -1 O MET A 300 N LEU A 120 SHEET 3 AA1 7 THR A 290 GLU A 295 -1 N TYR A 291 O PHE A 303 SHEET 4 AA1 7 THR A 281 ARG A 287 -1 N ALA A 283 O PHE A 294 SHEET 5 AA1 7 GLY A 271 ARG A 276 -1 N GLY A 271 O SER A 286 SHEET 6 AA1 7 PHE A 326 LEU A 333 -1 O LEU A 331 N ALA A 272 SHEET 7 AA1 7 MET A 243 LEU A 250 -1 N ASP A 248 O LEU A 328 CISPEP 1 PRO A 324 PRO A 325 0 2.23 CRYST1 56.139 63.041 65.461 90.00 90.00 90.00 P 21 21 21 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 0.017813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015863 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015276 0.00000 MASTER 267 0 0 13 7 0 0 6 2186 1 0 21 END