HEADER UNKNOWN FUNCTION 13-JUL-15 5CIV TITLE SIBLING LETHAL FACTOR PRECURSOR - DFSB COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIBLING BACTERIOCIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 13-184; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAENIBACILLUS DENDRITIFORMIS; SOURCE 3 ORGANISM_TAXID: 130049; SOURCE 4 GENE: DFSB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PQE-30 KEYWDS BACTERIOCIN, SPORULATION, DUF1706, CELL CYCLE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.D.TAYLOR,S.J.MATTHEWS REVDAT 2 02-MAR-16 5CIV 1 JRNL REVDAT 1 03-FEB-16 5CIV 0 JRNL AUTH J.D.TAYLOR,G.TAYLOR,S.A.HARE,S.J.MATTHEWS JRNL TITL STRUCTURES OF THE DFSB PROTEIN FAMILY SUGGEST A CATIONIC, JRNL TITL 2 HELICAL SIBLING LETHAL FACTOR PEPTIDE. JRNL REF J.MOL.BIOL. V. 428 554 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 26804569 JRNL DOI 10.1016/J.JMB.2016.01.013 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 32427 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) : 0.181 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1967 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 21.5112 - 3.3324 0.99 2439 159 0.1635 0.1746 REMARK 3 2 3.3324 - 2.6466 1.00 2338 151 0.1815 0.1689 REMARK 3 3 2.6466 - 2.3125 1.00 2324 150 0.1780 0.2336 REMARK 3 4 2.3125 - 2.1013 0.99 2270 150 0.1676 0.1957 REMARK 3 5 2.1013 - 1.9508 0.99 2269 145 0.1774 0.1859 REMARK 3 6 1.9508 - 1.8358 0.99 2241 144 0.1842 0.2093 REMARK 3 7 1.8358 - 1.7439 0.98 2258 143 0.1933 0.2375 REMARK 3 8 1.7439 - 1.6680 0.98 2226 143 0.1878 0.2049 REMARK 3 9 1.6680 - 1.6038 0.98 2203 143 0.1890 0.2146 REMARK 3 10 1.6038 - 1.5485 0.97 2198 145 0.1931 0.2226 REMARK 3 11 1.5485 - 1.5001 0.96 2179 140 0.2043 0.2158 REMARK 3 12 1.5001 - 1.4572 0.95 2168 136 0.2151 0.2324 REMARK 3 13 1.4572 - 1.4189 0.81 1824 122 0.2618 0.2584 REMARK 3 14 1.4189 - 1.3843 0.67 1523 96 0.2774 0.2757 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.740 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 : 0.006 1458 REMARK 3 ANGLE : 1.022 1977 REMARK 3 CHIRALITY : 0.042 200 REMARK 3 PLANARITY : 0.006 252 REMARK 3 DIHEDRAL : 13.958 540 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 5CIV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211713. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : 0.97880 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32427 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 21.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.02500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 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: SAD 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 (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 550 MME, 6% PEG 20,000, 0.1 M REMARK 280 SODIUM FORMATE; 0.1 M AMMONIUM ACETATE; 0.1 M SODIUM CITRATE REMARK 280 TRIBASIC DIHYDRATE; 0.1 M SODIUM POTASSIUM TARTRATE TETRAHYDRATE; REMARK 280 0.1 M SODIUM OXAMATE, 0.1 M TRIS, 0.1 M BICINE, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.79500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.84000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.79500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.84000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 ARG A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 ALA A 13 REMARK 465 SER A 14 REMARK 465 TYR A 15 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 416 O HOH A 428 1.81 REMARK 500 O HOH A 379 O HOH A 429 1.96 REMARK 500 O HOH A 262 O HOH A 328 1.98 REMARK 500 O HOH A 379 O HOH A 404 1.99 REMARK 500 O HOH A 319 O HOH A 375 2.02 REMARK 500 O HOH A 358 O HOH A 408 2.06 REMARK 500 NH1 ARG A 117 O HOH A 201 2.08 REMARK 500 O HOH A 220 O HOH A 265 2.14 REMARK 500 O HOH A 371 O HOH A 407 2.19 REMARK 500 O HOH A 209 O HOH A 369 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 SER A 163 -82.18 -143.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 5CIV A 13 184 UNP D0EVD3 D0EVD3_9BACL 2 173 SEQADV 5CIV MET A 1 UNP D0EVD3 INITIATING METHIONINE SEQADV 5CIV ARG A 2 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV GLY A 3 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV SER A 4 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV HIS A 5 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV HIS A 6 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV HIS A 7 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV HIS A 8 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV HIS A 9 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV HIS A 10 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV GLY A 11 UNP D0EVD3 EXPRESSION TAG SEQADV 5CIV SER A 12 UNP D0EVD3 EXPRESSION TAG SEQRES 1 A 184 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ALA SEQRES 2 A 184 SER TYR GLU TYR THR SER LYS GLU GLU LEU LYS LYS THR SEQRES 3 A 184 ILE HIS ALA ALA TYR LEU LEU LEU ASP GLY GLU PHE GLU SEQRES 4 A 184 GLY ILE ASP ASP SER GLN LYS ASP ASN ARG VAL PRO GLU SEQRES 5 A 184 VAL ASP ARG THR PRO ALA GLU ILE ILE ALA TYR GLN LEU SEQRES 6 A 184 GLY TRP LEU HIS LEU VAL MSE GLY TRP ASP ARG ASP GLU SEQRES 7 A 184 LEU ALA GLY LYS PRO VAL ILE MSE PRO ALA PRO GLY TYR SEQRES 8 A 184 LYS TRP ASN GLN LEU GLY GLY LEU TYR GLN SER PHE TYR SEQRES 9 A 184 ALA ALA TYR ALA ASP LEU SER LEU THR GLU LEU ARG ARG SEQRES 10 A 184 LEU PHE ARG ASP THR GLU ARG GLN TRP LEU ASP TRP ILE SEQRES 11 A 184 ASP THR LEU SER GLU GLU ASP LEU PHE THR GLN SER VAL SEQRES 12 A 184 ARG LYS TRP THR GLY ASP LYS PRO ASN TRP PRO MSE ALA SEQRES 13 A 184 ARG TRP ILE HIS ILE ASN SER ALA ALA PRO PHE LYS THR SEQRES 14 A 184 PHE ARG ALA LYS ILE ARG LYS TRP LYS LYS HIS GLN ARG SEQRES 15 A 184 GLN ALA MODRES 5CIV MSE A 72 MET MODIFIED RESIDUE MODRES 5CIV MSE A 86 MET MODIFIED RESIDUE MODRES 5CIV MSE A 155 MET MODIFIED RESIDUE HET MSE A 72 8 HET MSE A 86 8 HET MSE A 155 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *238(H2 O) HELIX 1 AA1 SER A 19 GLU A 37 1 19 HELIX 2 AA2 ASP A 42 LYS A 46 5 5 HELIX 3 AA3 THR A 56 GLY A 81 1 26 HELIX 4 AA4 LYS A 92 ASN A 94 5 3 HELIX 5 AA5 GLN A 95 ALA A 108 1 14 HELIX 6 AA6 SER A 111 THR A 132 1 22 HELIX 7 AA7 SER A 134 THR A 140 1 7 HELIX 8 AA8 PRO A 154 ILE A 161 1 8 HELIX 9 AA9 SER A 163 HIS A 180 1 18 LINK C VAL A 71 N MSE A 72 1555 1555 1.33 LINK C MSE A 72 N GLY A 73 1555 1555 1.33 LINK C ILE A 85 N MSE A 86 1555 1555 1.32 LINK C MSE A 86 N PRO A 87 1555 1555 1.34 LINK C PRO A 154 N MSE A 155 1555 1555 1.33 LINK C MSE A 155 N ALA A 156 1555 1555 1.33 CISPEP 1 MSE A 86 PRO A 87 0 1.06 CRYST1 47.590 47.680 72.300 90.00 90.00 90.00 P 21 21 21 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 0.021013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020973 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013831 0.00000