HEADER TOXIN 14-MAR-26 11VM TITLE EQTDI1 IMMUNITY PROTEIN MUTANT G152A COMPND MOL_ID: 1; COMPND 2 MOLECULE: TDI1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS QUEBECENSIS; SOURCE 3 ORGANISM_TAXID: 903983; SOURCE 4 GENE: BCR23_09875; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EFFECTOR, IMMUNITY, POLYMORPHIC TOXIN, SECRETION SYSTEM, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR B.DUROCHER,D.E.BOSCH REVDAT 1 30-SEP-26 11VM 0 JRNL AUTH R.ABBASIAN,B.PARAJULI,L.YU,B.DUROCHER,E.GARDNER,E.CHODUR, JRNL AUTH 2 M.K.DWELLEY,C.D.ELLERMEIER,T.D.HO,D.E.BOSCH JRNL TITL SECRETED NUCLEASE EFFECTOR NEUTRALIZATION BY ACTIVE SITE JRNL TITL 2 MIMICRY IN BACILLOTA. JRNL REF MBIO V. 17 51626 2026 JRNL REFN ESSN 2150-7511 JRNL PMID 42606298 JRNL DOI 10.1128/MBIO.01516-26 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.LIEBSCHNER,P.V.AFONINE,M.L.BAKER,G.BUNKOCZI,V.B.CHEN, REMARK 1 AUTH 2 T.I.CROLL,B.HINTZE,L.W.HUNG,S.JAIN,A.J.MCCOY,N.W.MORIARTY, REMARK 1 AUTH 3 R.D.OEFFNER,B.K.POON,M.G.PRISANT,R.J.READ,J.S.RICHARDSON, REMARK 1 AUTH 4 D.C.RICHARDSON,M.D.SAMMITO,O.V.SOBOLEV,D.H.STOCKWELL, REMARK 1 AUTH 5 T.C.TERWILLIGER,A.G.URZHUMTSEV,L.L.VIDEAU,C.J.WILLIAMS, REMARK 1 AUTH 6 P.D.ADAMS REMARK 1 TITL MACROMOLECULAR STRUCTURE DETERMINATION USING X-RAYS, REMARK 1 TITL 2 NEUTRONS AND ELECTRONS: RECENT DEVELOPMENTS IN PHENIX REMARK 1 REF ACTA CRYSTALLOGR D STRUCT 2019 REMARK 1 REF 2 BIOL REMARK 1 REFN REMARK 1 PMID 31588918 REMARK 1 DOI 10.1107/S2059798319011471 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 22548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1138 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 60.0800 - 3.4000 1.00 2786 142 0.1482 0.1864 REMARK 3 2 3.4000 - 2.7000 0.99 2678 135 0.1767 0.2081 REMARK 3 3 2.7000 - 2.3600 0.99 2675 145 0.1820 0.2390 REMARK 3 4 2.3600 - 2.1400 1.00 2661 143 0.2136 0.2586 REMARK 3 5 2.1400 - 1.9900 0.99 2648 155 0.1915 0.2461 REMARK 3 6 1.9900 - 1.8700 0.98 2585 154 0.2364 0.2899 REMARK 3 7 1.8700 - 1.7800 1.00 2684 125 0.1914 0.2378 REMARK 3 8 1.7800 - 1.7000 1.00 2693 139 0.1654 0.2124 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) : 0.182 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.988 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 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 : 0.011 1539 REMARK 3 ANGLE : 1.142 2084 REMARK 3 CHIRALITY : 0.066 224 REMARK 3 PLANARITY : 0.010 262 REMARK 3 DIHEDRAL : 12.735 569 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 2.3521 -7.9220 -23.6299 REMARK 3 T TENSOR REMARK 3 T11: 0.0990 T22: 0.1004 REMARK 3 T33: 0.1061 T12: 0.0292 REMARK 3 T13: -0.0013 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 0.9849 L22: 0.9857 REMARK 3 L33: 1.2848 L12: -0.0645 REMARK 3 L13: -0.0836 L23: 0.3505 REMARK 3 S TENSOR REMARK 3 S11: -0.0100 S12: -0.0187 S13: -0.0129 REMARK 3 S21: 0.0793 S22: 0.0928 S23: -0.0316 REMARK 3 S31: 0.1158 S32: 0.1561 S33: 0.0946 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 11VM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000306130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-24 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 : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22560 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 60.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 49.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 100 MM MAGNESIUM REMARK 280 CHLORIDE, 100 MM BIS-TRIS PROPANE PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+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 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 23.46949 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.28300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.69585 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.46949 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.28300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 37.69585 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 443 LIES ON A SPECIAL POSITION. 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 37 -61.42 -124.43 REMARK 500 THR A 104 169.47 63.71 REMARK 500 PRO A 126 48.07 -100.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 488 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 489 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A 490 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A 491 DISTANCE = 7.04 ANGSTROMS DBREF1 11VM A 1 180 UNP A0A1E5GR18_9ENTE DBREF2 11VM A A0A1E5GR18 1 180 SEQADV 11VM ALA A 152 UNP A0A1E5GR1 GLY 152 ENGINEERED MUTATION SEQRES 1 A 180 MET GLU LYS VAL LEU ASN ASP PHE LYS LEU GLU LYS LYS SEQRES 2 A 180 VAL PRO SER GLU LEU ILE ASP LYS TYR VAL ASN LEU VAL SEQRES 3 A 180 PRO GLU GLU ILE ILE VAL MET TRP LYS ASN TYR GLY PHE SEQRES 4 A 180 GLY THR PHE MET ASN GLY TYR PHE LYS SER ILE ASN PRO SEQRES 5 A 180 ASP ASP PHE LYS ASP ILE LEU LEU GLU THR SER GLN ARG SEQRES 6 A 180 TYR GLN ASP ALA ILE VAL LEU PHE ALA THR SER MET GLY SEQRES 7 A 180 ASP LEU ILE VAL TRP SER ASP ASP TYR VAL ARG LEU LEU SEQRES 8 A 180 ASN TYR ARG TYR GLY LYS VAL THR THR ILE LEU HIS THR SEQRES 9 A 180 PHE ASP PHE PHE PHE SER ASN ILE SER ASP LEU GLU PHE SEQRES 10 A 180 LYS ILE GLU ASP LEU HIS TRP LEU PRO TYR PRO ASP ALA SEQRES 11 A 180 ILE ALA ARG TYR GLY GLU PRO SER TYR ASP GLU CYS PHE SEQRES 12 A 180 GLY TYR VAL PRO ILE LEU GLY MET ALA GLY MET GLU LYS SEQRES 13 A 180 VAL GLU ASN LEU GLN LYS VAL LYS LEU ARG GLU HIS ILE SEQRES 14 A 180 LEU ILE ILE THR HIS PHE MET GLY PRO ILE LYS FORMUL 2 HOH *291(H2 O) HELIX 1 AA1 LYS A 3 PHE A 8 5 6 HELIX 2 AA2 PRO A 15 VAL A 23 1 9 HELIX 3 AA3 PRO A 27 TYR A 37 1 11 HELIX 4 AA4 ASN A 51 SER A 63 1 13 HELIX 5 AA5 PHE A 107 SER A 113 1 7 HELIX 6 AA6 ASP A 114 ASP A 121 1 8 HELIX 7 AA7 PRO A 126 GLY A 135 1 10 HELIX 8 AA8 ILE A 148 ALA A 152 5 5 HELIX 9 AA9 LYS A 156 GLU A 158 5 3 HELIX 10 AB1 LEU A 165 GLY A 177 1 13 SHEET 1 AA1 7 LYS A 9 LYS A 12 0 SHEET 2 AA1 7 PHE A 39 PHE A 42 -1 O PHE A 39 N GLU A 11 SHEET 3 AA1 7 PHE A 47 SER A 49 -1 O SER A 49 N GLY A 40 SHEET 4 AA1 7 ILE A 70 THR A 75 -1 O ALA A 74 N LYS A 48 SHEET 5 AA1 7 ASP A 79 SER A 84 -1 O ILE A 81 N LEU A 72 SHEET 6 AA1 7 TYR A 87 ASN A 92 -1 O LEU A 91 N LEU A 80 SHEET 7 AA1 7 LYS A 97 HIS A 103 -1 O THR A 99 N LEU A 90 SHEET 1 AA2 2 GLU A 141 TYR A 145 0 SHEET 2 AA2 2 LEU A 160 LYS A 164 -1 O VAL A 163 N CYS A 142 CISPEP 1 LEU A 125 PRO A 126 0 3.60 CISPEP 2 VAL A 146 PRO A 147 0 -8.88 CRYST1 70.775 38.566 79.070 90.00 107.55 90.00 I 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 0.014129 0.000000 0.004467 0.00000 SCALE2 0.000000 0.025930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013264 0.00000 MASTER 269 0 0 10 9 0 0 6 1785 1 0 14 END