HEADER TOXIN 09-FEB-20 6LWZ TITLE CRYSTAL STRUCTURE OF LATEROSPORULIN10, BACTERIOCIN PRODUCED BY TITLE 2 BREVIBACILLUS SP. STRAIN SKDU10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOCIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BREVIBACILLUS SP. SKDU10; SOURCE 3 ORGANISM_TAXID: 1247872 KEYWDS BACTERIOCIN, ANTIMICROBIAL PEPTIDE, BREVIBACILLUS, LATEROSPORULIN, KEYWDS 2 TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR K.G.THAKUR,V.SOLANKI REVDAT 3 16-OCT-24 6LWZ 1 REMARK REVDAT 2 29-NOV-23 6LWZ 1 REMARK REVDAT 1 10-FEB-21 6LWZ 0 JRNL AUTH K.G.THAKUR,V.SOLANKI JRNL TITL CRYSTAL STRUCTURE OF LATEROSPORULIN10, BACTERIOCIN PRODUCED JRNL TITL 2 BY BREVIBACILLUS SP. STRAIN SKDU10 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0218 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 3486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 363 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 237 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 842 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.82000 REMARK 3 B22 (A**2) : 1.47000 REMARK 3 B33 (A**2) : -0.58000 REMARK 3 B12 (A**2) : 1.21000 REMARK 3 B13 (A**2) : 0.57000 REMARK 3 B23 (A**2) : 1.28000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 868 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1172 ; 2.184 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 104 ; 5.725 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ;35.486 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 148 ;16.790 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;13.720 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 116 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 662 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6LWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3487 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 29.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : 0.49300 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: PHASER REMARK 200 STARTING MODEL: 4OZK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 21.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CALCIUM CHLORIDE, 0.1 M SODIUM REMARK 280 CACODYLATE PH 5.5, 12 % PEG W/V 8000 AND 3 % W/V TRIMETHYLAMINE REMARK 280 N-OXIDE DIHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ASN A 38 -74.79 -61.70 REMARK 500 GLN A 40 -119.92 -129.62 REMARK 500 CYS A 44 -63.26 -102.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 6LWZ A 2 54 PDB 6LWZ 6LWZ 2 54 DBREF 6LWZ B 2 54 PDB 6LWZ 6LWZ 2 54 SEQRES 1 A 53 ALA CYS VAL ASN GLN CYS PRO ASP ALA ILE ASP ARG PHE SEQRES 2 A 53 ILE VAL LYS ASP LYS GLY CYS HIS GLY VAL GLU LYS LYS SEQRES 3 A 53 TYR TYR LYS GLN VAL TYR VAL ALA CYS MET ASN GLY GLN SEQRES 4 A 53 HIS LEU TYR CYS ARG THR GLU TRP GLY GLY PRO CYS GLN SEQRES 5 A 53 LEU SEQRES 1 B 53 ALA CYS VAL ASN GLN CYS PRO ASP ALA ILE ASP ARG PHE SEQRES 2 B 53 ILE VAL LYS ASP LYS GLY CYS HIS GLY VAL GLU LYS LYS SEQRES 3 B 53 TYR TYR LYS GLN VAL TYR VAL ALA CYS MET ASN GLY GLN SEQRES 4 B 53 HIS LEU TYR CYS ARG THR GLU TRP GLY GLY PRO CYS GLN SEQRES 5 B 53 LEU FORMUL 3 HOH *14(H2 O) SHEET 1 AA1 6 HIS A 41 PRO A 51 0 SHEET 2 AA1 6 LYS A 27 CYS A 36 -1 N TYR A 28 O GLY A 49 SHEET 3 AA1 6 ILE A 11 CYS A 21 -1 N ARG A 13 O ALA A 35 SHEET 4 AA1 6 ILE B 11 CYS B 21 1 O ASP B 18 N ASP A 18 SHEET 5 AA1 6 LYS B 27 CYS B 36 -1 O ALA B 35 N ASP B 12 SHEET 6 AA1 6 HIS B 41 PRO B 51 -1 O GLY B 49 N TYR B 28 SSBOND 1 CYS A 3 CYS A 44 1555 1555 1.86 SSBOND 2 CYS A 7 CYS A 36 1555 1555 2.03 SSBOND 3 CYS A 21 CYS A 52 1555 1555 2.02 SSBOND 4 CYS B 3 CYS B 44 1555 1555 2.03 SSBOND 5 CYS B 7 CYS B 36 1555 1555 2.03 SSBOND 6 CYS B 21 CYS B 52 1555 1555 2.18 CRYST1 22.280 29.340 32.150 110.62 89.99 104.94 P 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 0.044883 0.011976 0.004679 0.00000 SCALE2 0.000000 0.035276 0.013805 0.00000 SCALE3 0.000000 0.000000 0.033401 0.00000 TER 422 LEU A 54 TER 844 LEU B 54 HETATM 845 O HOH A 101 -3.937 -1.041 3.532 1.00 31.93 O HETATM 846 O HOH A 102 23.666 13.695 4.659 1.00 38.22 O HETATM 847 O HOH A 103 21.470 12.062 4.977 1.00 41.10 O HETATM 848 O HOH A 104 18.418 15.014 -9.599 1.00 38.02 O HETATM 849 O HOH A 105 16.648 19.602 4.487 1.00 41.37 O HETATM 850 O HOH A 106 1.672 1.402 -6.730 1.00 28.02 O HETATM 851 O HOH A 107 14.327 6.496 6.838 1.00 48.26 O HETATM 852 O HOH A 108 -1.147 3.549 9.783 1.00 37.48 O HETATM 853 O HOH A 109 24.779 27.876 2.093 1.00 39.05 O HETATM 854 O HOH A 110 11.805 21.585 -2.784 1.00 40.96 O HETATM 855 O HOH B 101 0.085 28.802 16.274 1.00 34.80 O HETATM 856 O HOH B 102 19.522 4.366 15.677 1.00 31.25 O HETATM 857 O HOH B 103 27.020 2.279 13.369 1.00 33.97 O HETATM 858 O HOH B 104 25.380 15.249 11.952 1.00 14.05 O CONECT 11 342 CONECT 41 277 CONECT 150 404 CONECT 277 41 CONECT 342 11 CONECT 404 150 CONECT 433 764 CONECT 463 699 CONECT 572 826 CONECT 699 463 CONECT 764 433 CONECT 826 572 MASTER 250 0 0 0 6 0 0 6 856 2 12 10 END