HEADER TOXIN/ANTITOXIN 06-SEP-21 7VD7 TITLE TOXIN - ANTITOXIN COMPLEX FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BRNT FAMILY TOXIN, MEMBRANE PROTEIN,PUTATIVE INNER MEMBRANE COMPND 5 PROTEIN,RIBONUCLEASE TOXIN,BRNT,OF TYPE II TOXIN-ANTITOXIN SYSTEM; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ANTITOXIN; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: BRNA ANTITOXIN FAMILY PROTEIN, BRNA ANTITOXIN OF TYPE II COMPND 12 TOXIN-ANTITOXIN SYSTEM,PUTATIVE CYTOPLASMIC PROTEIN,TOXIN-ANTITOXIN COMPND 13 SYSTEM,ANTITOXIN COMPONENT; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_COMMON: SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SOURCE 4 ORGANISM_TAXID: 90371; SOURCE 5 STRAIN: 14028S; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 10 ORGANISM_COMMON: SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SOURCE 11 ORGANISM_TAXID: 90371; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN-ANTITOXIN COMPLEX RIBONUCLEASE, TOXIN, TOXIN-ANTITOXIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.-J.EUN,B.-J.LEE,S.-W.JANG,J.-H.PARK REVDAT 3 03-APR-24 7VD7 1 REMARK REVDAT 2 28-SEP-22 7VD7 1 JRNL REVDAT 1 14-SEP-22 7VD7 0 JRNL AUTH H.-J.EUN,S.-W.JANG,J.-H.PARK,B.-J.LEE JRNL TITL TOXIN-ANTITOXIN COMPLEX FROM SALMONELLA ENTERICA SEROVAR JRNL TITL 2 TYPHIMURIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 19672 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1054 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1475 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1137 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : 0.84000 REMARK 3 B33 (A**2) : -0.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.323 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1162 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1080 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1560 ; 1.730 ; 1.643 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2478 ; 1.482 ; 1.595 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 136 ; 6.226 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;32.968 ;20.617 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 205 ;15.344 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.953 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 138 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1320 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 300 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 550 ; 2.106 ; 1.895 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 549 ; 2.072 ; 1.891 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 684 ; 2.952 ; 2.835 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 685 ; 2.954 ; 2.838 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 612 ; 3.253 ; 2.296 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 613 ; 3.250 ; 2.297 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 877 ; 4.885 ; 3.301 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1349 ; 6.363 ;24.359 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1322 ; 6.338 ;23.838 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7VD7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300024517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-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 : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97959 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20736 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 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 1.19.2-4158 REMARK 200 STARTING MODEL: NO PDB ENTRY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 6000 100 MM HEPES/ REMARK 280 SODIUM HYDROXIDE PH 7.0 200 MM SODIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 15.80250 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 DBREF1 7VD7 A 2 95 UNP A0A0F7JD05_SALTM DBREF2 7VD7 A A0A0F7JD05 2 95 DBREF1 7VD7 B 14 57 UNP A0A0F7JDL4_SALTM DBREF2 7VD7 B A0A0F7JDL4 14 57 SEQADV 7VD7 ASP A 74 UNP A0A0F7JD0 GLU 74 ENGINEERED MUTATION SEQRES 1 A 94 PRO MET GLU PHE GLU TRP ASP ALA ASN LYS ALA LYS SER SEQRES 2 A 94 ASN LEU ARG LYS HIS GLY VAL ARG PHE GLU ASP ALA VAL SEQRES 3 A 94 LEU VAL PHE ASP ASP PRO ARG HIS LEU SER ARG GLN GLU SEQRES 4 A 94 ARG TYR GLU ASN GLY GLU TYR ARG TRP GLN THR LEU GLY SEQRES 5 A 94 LEU VAL HIS GLY ILE VAL VAL ILE LEU VAL ALA HIS SER SEQRES 6 A 94 VAL ARG PHE GLU SER GLY PHE ASP VAL ILE ARG ILE ILE SEQRES 7 A 94 SER ALA ARG LYS ALA ASP ARG LYS GLU ARG ASN ARG TYR SEQRES 8 A 94 GLU HIS GLY SEQRES 1 B 44 LEU SER ALA GLN HIS GLU ALA GLU LEU LYS ALA LEU ALA SEQRES 2 B 44 LYS LYS SER ASP ASP GLU ILE ASP TYR SER ASP ILE PRO SEQRES 3 B 44 ALA SER GLU ASP GLY GLN TRP SER GLU ALA VAL ARG GLY SEQRES 4 B 44 LYS PHE PHE ARG PRO FORMUL 3 HOH *145(H2 O) HELIX 1 AA1 ASP A 8 GLY A 20 1 13 HELIX 2 AA2 ARG A 22 VAL A 27 1 6 HELIX 3 AA3 LEU A 28 ASP A 32 5 5 HELIX 4 AA4 ASP A 85 GLY A 95 1 11 HELIX 5 AA5 SER B 15 LYS B 27 1 13 HELIX 6 AA6 LYS B 28 ILE B 33 5 6 HELIX 7 AA7 GLU B 42 SER B 47 5 6 SHEET 1 AA1 6 MET A 3 GLU A 6 0 SHEET 2 AA1 6 ASP A 74 LYS A 83 1 O ILE A 76 N GLU A 4 SHEET 3 AA1 6 VAL A 59 PHE A 69 -1 N LEU A 62 O ARG A 82 SHEET 4 AA1 6 GLU A 46 VAL A 55 -1 N TRP A 49 O HIS A 65 SHEET 5 AA1 6 LEU A 36 GLU A 43 -1 N ARG A 41 O ARG A 48 SHEET 6 AA1 6 VAL B 50 ARG B 51 -1 O VAL B 50 N SER A 37 CRYST1 39.366 31.605 47.985 90.00 90.63 90.00 P 1 21 1 2 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 0.025403 0.000000 0.000279 0.00000 SCALE2 0.000000 0.031641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020841 0.00000