HEADER HYDROLASE 09-DEC-23 8XCL TITLE CHARACTER OF TSEP: A DUAL FUNCTIONAL EFFECTOR OF TYPE VI SECRETION TITLE 2 SYSTEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: EF-HAND DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TSEP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROMONAS DHAKENSIS; SOURCE 3 ORGANISM_TAXID: 196024; SOURCE 4 GENE: HMPREF1171_00947; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS T6SS, INTERSPECIES INTERACTION, BIFUNCTIONAL EFFECTOR, PEPTIDOGLYCAN KEYWDS 2 HYDROLYSIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.M.QIN,T.ZHAO,T.DONG,Z.H.WANG REVDAT 1 23-APR-25 8XCL 0 JRNL AUTH Z.H.WANG,Y.AN,T.ZHAO,T.T.PEI,D.Y.WANG,X.LIANG,W.QIN,T.DONG JRNL TITL AMIDASE AND LYSOZYME DUAL FUNCTIONS IN TSEP REVEAL A NEW JRNL TITL 2 FAMILY OF CHIMERIC EFFECTORS IN THE TYPE VI SECRETION JRNL TITL 3 SYSTEM. JRNL REF ELIFE V. 13 2025 JRNL REFN ESSN 2050-084X JRNL PMID 40063082 JRNL DOI 10.7554/ELIFE.101125 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16-3549 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14135 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 708 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 47.9000 - 3.8807 1.00 2802 149 0.1859 0.2073 REMARK 3 2 3.8807 - 3.0804 1.00 2706 142 0.1766 0.2217 REMARK 3 3 3.0804 - 2.6911 1.00 2654 140 0.1932 0.2441 REMARK 3 4 2.6911 - 2.4450 1.00 2642 139 0.1912 0.2572 REMARK 3 5 2.4450 - 2.2700 1.00 2623 138 0.2052 0.2594 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.210 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 : 0.007 1956 REMARK 3 ANGLE : 0.871 2638 REMARK 3 CHIRALITY : 0.050 272 REMARK 3 PLANARITY : 0.005 345 REMARK 3 DIHEDRAL : 6.135 1161 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 8XCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043204. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25776 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 48.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.21800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.77100 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: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM FORMATE PH 7.0 ,12% W/V REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 47.91350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.91350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.24050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.39850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.24050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.39850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.91350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.24050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.39850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.91350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.24050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.39850 REMARK 290 SMTRY3 8 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 417 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 421 LIES ON A SPECIAL POSITION. 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 GLY A 3 REMARK 465 THR A 4 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 LEU A 145 -61.44 -96.83 REMARK 500 HIS A 150 156.04 82.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 8XCL A 3 246 UNP K1JFN7 K1JFN7_9GAMM 602 845 SEQADV 8XCL THR A 4 UNP K1JFN7 GLY 603 CONFLICT SEQRES 1 A 244 GLY THR ASP LEU ILE THR LEU GLU MET VAL PHE ALA ALA SEQRES 2 A 244 ASN LEU ASN GLN ASP LYS SER SER CYS GLU ALA ILE LEU SEQRES 3 A 244 PRO PHE LEU ASN GLU TYR ALA LYS THR TYR GLY MET LYS SEQRES 4 A 244 GLU GLU ARG ALA MET ALA HIS PHE LEU SER GLN VAL GLY SEQRES 5 A 244 HIS GLU SER ASN PHE LYS PRO VAL SER GLU ASN LEU ARG SEQRES 6 A 244 TYR SER PRO LYS GLY MET ARG LYS ILE PHE GLY CYS LYS SEQRES 7 A 244 GLY GLY SER LYS ASN TYR ASP PRO ILE LEU ASP ASP ALA SEQRES 8 A 244 LYS GLU GLY ARG LEU ARG PRO LYS LEU TRP THR HIS GLU SEQRES 9 A 244 SER ASP TYR ALA PHE ASN PRO VAL ALA LEU GLY ASN TYR SEQRES 10 A 244 VAL TYR ALA ASN ARG PRO GLY SER LYS ASN GLY ASP GLU SEQRES 11 A 244 SER SER GLY ASP GLY TYR LYS TYR ARG GLY ARG GLY LEU SEQRES 12 A 244 ILE GLN ILE THR HIS LYS ASP ALA TYR ILE LYS PHE THR SEQRES 13 A 244 GLU ALA HIS ASN ALA ALA ASN PRO SER ASP GLN LYS ASP SEQRES 14 A 244 PHE LEU ALA SER PRO ASP ASP ILE LEU THR LEU ARG TYR SEQRES 15 A 244 ALA THR SER SER ALA TYR PHE PHE TRP PHE ILE TYR LYS SEQRES 16 A 244 LYS SER PHE ASN LEU HIS SER THR ALA CYS THR GLY THR SEQRES 17 A 244 VAL LYS GLU VAL THR LYS ILE VAL ASN GLY GLY TYR ALA SEQRES 18 A 244 GLY TYR ALA ASP ARG LEU LYS ARG PHE ASN ALA VAL ALA SEQRES 19 A 244 ALA VAL ILE GLY ILE ASP GLY ALA ARG GLU FORMUL 2 HOH *123(H2 O) HELIX 1 AA1 THR A 8 ASN A 16 1 9 HELIX 2 AA2 ASP A 20 GLY A 39 1 20 HELIX 3 AA3 GLU A 42 ASN A 58 1 17 HELIX 4 AA4 SER A 69 GLY A 78 1 10 HELIX 5 AA5 GLY A 82 LYS A 84 5 3 HELIX 6 AA6 PRO A 100 HIS A 105 1 6 HELIX 7 AA7 HIS A 105 ALA A 110 1 6 HELIX 8 AA8 ASN A 112 TYR A 121 1 10 HELIX 9 AA9 ASP A 131 SER A 134 5 4 HELIX 10 AB1 GLY A 135 TYR A 140 1 6 HELIX 11 AB2 HIS A 150 ASN A 165 1 16 HELIX 12 AB3 SER A 175 LEU A 180 5 6 HELIX 13 AB4 THR A 181 ILE A 195 1 15 HELIX 14 AB5 LYS A 197 PHE A 200 5 4 HELIX 15 AB6 ASN A 201 GLY A 209 1 9 HELIX 16 AB7 THR A 210 GLY A 220 1 11 HELIX 17 AB8 GLY A 224 GLY A 240 1 17 SHEET 1 AA1 2 VAL A 62 SER A 63 0 SHEET 2 AA1 2 ARG A 143 GLY A 144 -1 O GLY A 144 N VAL A 62 SHEET 1 AA2 2 TYR A 86 ASP A 87 0 SHEET 2 AA2 2 ASP A 92 ALA A 93 -1 O ASP A 92 N ASP A 87 CRYST1 44.481 138.797 95.827 90.00 90.00 90.00 C 2 2 21 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 0.022482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010435 0.00000 MASTER 244 0 0 17 4 0 0 6 2033 1 0 19 END