HEADER TOXIN 13-MAR-26 11VH TITLE EQTDI1 IMMUNITY PROTEIN MUTANT M151L 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 11VH 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 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 21625 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.240 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 37.3600 - 4.1000 0.96 1433 145 0.1797 0.2084 REMARK 3 2 4.1000 - 3.2500 0.97 1403 143 0.1682 0.2092 REMARK 3 3 3.2500 - 2.8400 0.98 1403 143 0.1910 0.2611 REMARK 3 4 2.8400 - 2.5800 0.98 1411 143 0.1993 0.2321 REMARK 3 5 2.5800 - 2.4000 0.99 1403 143 0.2103 0.2369 REMARK 3 6 2.4000 - 2.2500 0.97 1392 141 0.2049 0.3072 REMARK 3 7 2.2500 - 2.1400 0.97 1388 142 0.2129 0.2674 REMARK 3 8 2.1400 - 2.0500 0.99 1416 144 0.2272 0.2972 REMARK 3 9 2.0500 - 1.9700 0.99 1369 140 0.2194 0.2846 REMARK 3 10 1.9700 - 1.9000 0.99 1397 142 0.2342 0.2847 REMARK 3 11 1.9000 - 1.8400 0.99 1400 142 0.2478 0.3206 REMARK 3 12 1.8400 - 1.7900 0.99 1409 144 0.2664 0.3102 REMARK 3 13 1.7900 - 1.7400 0.99 1399 143 0.2684 0.3242 REMARK 3 14 1.7400 - 1.7000 0.99 1404 143 0.2755 0.3123 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 0.012 1527 REMARK 3 ANGLE : 1.222 2071 REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 11VH 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_1000306131. 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 : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21631 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 37.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 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) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.74000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 (%): 47.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 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: 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 44.07150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.97950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.07150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.97950 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 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 382 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 MET A 1 REMARK 465 GLU A 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 204 O HOH A 344 2.17 REMARK 500 O HOH A 212 O HOH A 336 2.18 REMARK 500 O HOH A 225 O HOH A 354 2.18 REMARK 500 OE2 GLU A 158 O HOH A 201 2.19 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 TYR A 37 -62.26 -126.09 REMARK 500 MET A 43 66.79 66.90 REMARK 500 THR A 104 167.53 67.73 REMARK 500 PRO A 126 41.89 -102.99 REMARK 500 REMARK 500 REMARK: NULL DBREF1 11VH A 1 180 UNP A0A1E5GR18_9ENTE DBREF2 11VH A A0A1E5GR18 1 180 SEQADV 11VH LEU A 151 UNP A0A1E5GR1 MET 151 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 LEU GLY 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 *222(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 ASP A 54 5 4 HELIX 5 AA5 PHE A 55 SER A 63 1 9 HELIX 6 AA6 PHE A 107 SER A 113 1 7 HELIX 7 AA7 ASP A 114 ASP A 121 1 8 HELIX 8 AA8 PRO A 126 GLY A 135 1 10 HELIX 9 AA9 ILE A 148 GLY A 152 5 5 HELIX 10 AB1 LYS A 156 GLU A 158 5 3 HELIX 11 AB2 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 LYS A 97 N ASN A 92 SHEET 1 AA2 2 GLU A 141 TYR A 145 0 SHEET 2 AA2 2 LEU A 160 LYS A 164 -1 O GLN A 161 N GLY A 144 CISPEP 1 LEU A 125 PRO A 126 0 4.62 CISPEP 2 VAL A 146 PRO A 147 0 -4.56 CRYST1 88.143 37.959 70.392 90.00 122.04 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 0.011345 0.000000 0.007100 0.00000 SCALE2 0.000000 0.026344 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016759 0.00000 MASTER 252 0 0 11 9 0 0 6 1698 1 0 14 END