HEADER ANTIMICROBIAL PROTEIN 03-DEC-24 9HKJ TITLE STRUCTURE OF FORMOSIN D COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOCOCCIN 972 FAMILY BACTERIOCIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS DSM 13 = ATCC 14580; SOURCE 3 ORGANISM_TAXID: 279010; SOURCE 4 STRAIN: DSM 13 KEYWDS LACTOCOCCIN, BACTERIOCIN, FORMOSIN D, BACILLUS LICHENIFORMIS, KEYWDS 2 ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.J.PALM,M.LAMMERS REVDAT 1 17-DEC-25 9HKJ 0 JRNL AUTH A.HILKMANN,G.J.PALM,M.LAMMERS,T.SCHWEDER JRNL TITL A HIGHLY EXPRESSED ANTIMICROBIAL PROTEIN PRODUCED BY JRNL TITL 2 BACILLUS LICHENIFORMIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 8790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.858 REMARK 3 FREE R VALUE TEST SET COUNT : 427 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 629 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 682 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38100 REMARK 3 B22 (A**2) : 0.01300 REMARK 3 B33 (A**2) : -0.36300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.916 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 729 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 629 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 988 ; 1.448 ; 1.821 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1438 ; 0.479 ; 1.771 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 86 ; 9.040 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 6 ; 6.444 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 103 ;10.595 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 93 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 911 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 197 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 122 ; 0.175 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 28 ; 0.239 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 334 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 70 ; 0.154 ; 0.200 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): 348 ; 0.756 ; 0.949 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 344 ; 0.718 ; 0.935 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 430 ; 1.183 ; 1.670 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 431 ; 1.183 ; 1.674 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 381 ; 1.360 ; 1.115 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 374 ; 1.314 ; 1.101 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 558 ; 2.123 ; 1.972 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 547 ; 2.121 ; 1.941 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Ap 42 Ap 206 REMARK 3 ORIGIN FOR THE GROUP (A): 8.6990 0.1389 11.2452 REMARK 3 T TENSOR REMARK 3 T11: 0.0113 T22: 0.0422 REMARK 3 T33: 0.0034 T12: -0.0033 REMARK 3 T13: 0.0004 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.0484 L22: 0.6117 REMARK 3 L33: 0.6668 L12: -0.1308 REMARK 3 L13: -0.1240 L23: 0.2015 REMARK 3 S TENSOR REMARK 3 S11: 0.0108 S12: -0.0187 S13: 0.0043 REMARK 3 S21: -0.0673 S22: -0.0109 S23: 0.0076 REMARK 3 S31: 0.0224 S32: 0.0043 S33: 0.0002 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9HKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292143425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JUN 30, 2023 REMARK 200 DATA SCALING SOFTWARE : XSCALE VERSION JUN 30, 2023 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8801 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 46.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.19900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.22500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 UL WELL (15% PEG8000, 0.1 M MES PH REMARK 280 6.5, 0.2 M NAOAC) + 2 UL PROTEIN (1 MG/ML PROTEIN IN 200 MM NACL REMARK 280 100 MM TRIS PH 7.5), CRYO: WELL + 10% PEG400, VAPOR DIFFUSION, REMARK 280 HANGING 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 20.90150 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 DBREF 9HKJ A 42 126 UNP Q65CU4 Q65CU4_BACLD 42 126 SEQRES 1 A 85 TRP VAL ASN PRO GLY TYR HIS TYR GLN TYR PRO SER GLU SEQRES 2 A 85 GLY GLY THR TRP ARG TYR GLY PHE VAL ASN ALA GLY LEU SEQRES 3 A 85 ARG SER GLU TYR ASN HIS PRO THR LYS VAL HIS GLY SER SEQRES 4 A 85 THR VAL GLN LYS LEU ILE ASP GLY LYS VAL ASP LYS THR SEQRES 5 A 85 ASN ARG SER ILE ASP THR ALA ALA GLY ARG TYR SER ASN SEQRES 6 A 85 ALA TYR VAL GLY ALA ILE ASN SER PRO GLY LEU LYS GLY SEQRES 7 A 85 ARG TYR TYR TYR ARG THR ASN HET ACT A 201 7 HET ACT A 202 7 HET ACT A 203 7 HET ACT A 204 7 HET CL A 205 1 HET CL A 206 1 HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION FORMUL 2 ACT 4(C2 H3 O2 1-) FORMUL 6 CL 2(CL 1-) FORMUL 8 HOH *108(H2 O) SHEET 1 AA1 4 HIS A 48 GLN A 50 0 SHEET 2 AA1 4 THR A 57 VAL A 63 -1 O TYR A 60 N HIS A 48 SHEET 3 AA1 4 GLY A 66 ASN A 72 -1 O GLU A 70 N ARG A 59 SHEET 4 AA1 4 ALA A 107 GLY A 110 -1 O VAL A 109 N LEU A 67 SHEET 1 AA2 3 LYS A 89 ARG A 95 0 SHEET 2 AA2 3 HIS A 78 ILE A 86 -1 N LYS A 84 O ASP A 91 SHEET 3 AA2 3 LEU A 117 THR A 125 -1 O ARG A 120 N GLN A 83 CRYST1 21.020 41.803 46.758 90.00 96.61 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 0.047574 0.000000 0.005512 0.00000 SCALE2 0.000000 0.023922 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021530 0.00000 CONECT 1354 1355 1356 1357 CONECT 1355 1354 CONECT 1356 1354 CONECT 1357 1354 1358 1359 1360 CONECT 1358 1357 CONECT 1359 1357 CONECT 1360 1357 CONECT 1361 1362 1363 1364 CONECT 1362 1361 CONECT 1363 1361 CONECT 1364 1361 1365 1366 1367 CONECT 1365 1364 CONECT 1366 1364 CONECT 1367 1364 CONECT 1368 1369 1370 1371 CONECT 1369 1368 CONECT 1370 1368 CONECT 1371 1368 1372 1373 1374 CONECT 1372 1371 CONECT 1373 1371 CONECT 1374 1371 CONECT 1375 1376 1377 1378 CONECT 1376 1375 CONECT 1377 1375 CONECT 1378 1375 1379 1380 1381 CONECT 1379 1378 CONECT 1380 1378 CONECT 1381 1378 MASTER 251 0 6 0 7 0 0 6 808 1 28 7 END