HEADER HYDROLASE 20-JUL-12 4G76 TITLE STRUCTURE OF PAEM, A COLICIN M-LIKE BACTERIOCIN PRODUCED BY TITLE 2 PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: EXA13, PAEM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COLICIN-M LIKE, PHOSPHODIESTERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.TOUZE,M.GRAILLE,D.MENGIN-LECREULX REVDAT 6 06-DEC-23 4G76 1 REMARK REVDAT 5 13-SEP-23 4G76 1 SEQADV LINK REVDAT 4 14-NOV-12 4G76 1 JRNL REVDAT 3 07-NOV-12 4G76 1 TITLE REVDAT 2 26-SEP-12 4G76 1 JRNL REVDAT 1 12-SEP-12 4G76 0 JRNL AUTH H.BARRETEAU,M.TIOUAJNI,M.GRAILLE,N.JOSSEAUME,A.BOUHSS, JRNL AUTH 2 D.PATIN,D.BLANOT,M.FOURGEAUD,J.L.MAINARDI,M.ARTHUR, JRNL AUTH 3 H.VAN TILBEURGH,D.MENGIN-LECREULX,T.TOUZE JRNL TITL FUNCTIONAL AND STRUCTURAL CHARACTERIZATION OF PAEM, A JRNL TITL 2 COLICIN M-LIKE BACTERIOCIN PRODUCED BY PSEUDOMONAS JRNL TITL 3 AERUGINOSA. JRNL REF J.BIOL.CHEM. V. 287 37395 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22977250 JRNL DOI 10.1074/JBC.M112.406439 REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 22834 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1135 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 36.8556 - 4.7660 0.98 2761 148 0.1758 0.2033 REMARK 3 2 4.7660 - 3.7842 0.98 2787 143 0.1412 0.2230 REMARK 3 3 3.7842 - 3.3062 0.99 2768 144 0.1570 0.2192 REMARK 3 4 3.3062 - 3.0040 0.99 2805 149 0.1699 0.2687 REMARK 3 5 3.0040 - 2.7888 0.99 2812 149 0.1888 0.2548 REMARK 3 6 2.7888 - 2.6244 0.97 2771 141 0.1757 0.2679 REMARK 3 7 2.6244 - 2.4930 0.96 2733 142 0.1734 0.2664 REMARK 3 8 2.4930 - 2.3845 0.81 2262 119 0.2030 0.3260 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 : 0.36 REMARK 3 B_SOL : 27.39 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.710 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) : -8.13740 REMARK 3 B22 (A**2) : 10.27240 REMARK 3 B33 (A**2) : -2.13500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 2372 REMARK 3 ANGLE : 0.898 3242 REMARK 3 CHIRALITY : 0.060 332 REMARK 3 PLANARITY : 0.005 429 REMARK 3 DIHEDRAL : 17.894 831 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 4G76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22837 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4G75 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH7.5; 2M SODIUM FORMATE, REMARK 280 VAPOR 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 21.40600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.84650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.84650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.40600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.20000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MSE A 1 REMARK 465 VAL A 2 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 REMARK 465 HIS A 297 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 237 CZ 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 118 65.90 -118.94 REMARK 500 ASP A 130 99.99 -69.17 REMARK 500 ASP A 193 103.51 -166.48 REMARK 500 THR A 210 -55.46 -121.07 REMARK 500 SER A 288 -175.72 -178.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G75 RELATED DB: PDB DBREF 4G76 A 1 289 UNP Q1W548 Q1W548_PSEAI 1 289 SEQADV 4G76 ARG A 290 UNP Q1W548 EXPRESSION TAG SEQADV 4G76 SER A 291 UNP Q1W548 EXPRESSION TAG SEQADV 4G76 HIS A 292 UNP Q1W548 EXPRESSION TAG SEQADV 4G76 HIS A 293 UNP Q1W548 EXPRESSION TAG SEQADV 4G76 HIS A 294 UNP Q1W548 EXPRESSION TAG SEQADV 4G76 HIS A 295 UNP Q1W548 EXPRESSION TAG SEQADV 4G76 HIS A 296 UNP Q1W548 EXPRESSION TAG SEQADV 4G76 HIS A 297 UNP Q1W548 EXPRESSION TAG SEQRES 1 A 297 MSE VAL MSE ASP LEU GLY THR THR THR ILE VAL ALA GLY SEQRES 2 A 297 GLN GLY ASP PHE SER ALA TYR ASN TYR GLY ASN ASN GLY SEQRES 3 A 297 ALA ASN TRP PRO ALA PRO SER PRO ALA GLN VAL GLY TYR SEQRES 4 A 297 ILE SER LYS GLY GLN ARG ASP VAL ALA TYR VAL ASN GLY SEQRES 5 A 297 ASP TRP GLU LYS PRO LEU LEU ALA LEU TRP ALA GLN TRP SEQRES 6 A 297 ALA ASN TRP GLY THR THR LEU TYR GLY TYR PRO SER LEU SEQRES 7 A 297 PRO PHE PRO ASN TYR GLU PHE ILE TRP ASP ILE PHE ASP SEQRES 8 A 297 LEU PRO GLN ALA ASP TYR ASN GLN PHE SER LEU GLY ASP SEQRES 9 A 297 ASP ARG ILE THR ALA MSE ASN ARG ALA GLN ASN HIS GLN SEQRES 10 A 297 TYR PRO PHE PRO ASN ASN GLU GLY ILE PRO SER TRP ASP SEQRES 11 A 297 ARG PRO LYS ILE ASP THR PHE ASN GLY GLY VAL TYR THR SEQRES 12 A 297 PRO ALA ALA ALA PHE ALA HIS TYR LEU THR GLY LYS GLY SEQRES 13 A 297 LYS LYS MSE ASN PHE PRO ILE GLU ARG LEU ASN ILE LYS SEQRES 14 A 297 PRO ASN VAL LYS ALA MSE PRO GLN PHE ILE GLY VAL LEU SEQRES 15 A 297 THR SER SER PRO MSE GLY GLN THR THR VAL ASP PHE ASN SEQRES 16 A 297 VAL PRO TYR ALA THR ALA LYS ASP SER TRP VAL ALA GLY SEQRES 17 A 297 ASN THR VAL GLY GLU ILE THR LEU ARG ILE VAL GLY ILE SEQRES 18 A 297 LEU VAL LYS SER THR SER GLY GLN TRP SER PHE ARG GLY SEQRES 19 A 297 GLU ILE ARG ALA TYR ASP ASP LEU TYR ASP PHE ASN PRO SEQRES 20 A 297 SER ASN HIS ARG THR GLU THR ALA GLU GLY MSE THR ARG SEQRES 21 A 297 LEU GLY ARG GLU VAL GLY GLN LYS PHE LYS ASP THR THR SEQRES 22 A 297 PRO TYR PRO ILE GLY ILE PRO GLY ALA ILE PRO VAL ASN SEQRES 23 A 297 ILE SER GLY ARG SER HIS HIS HIS HIS HIS HIS MODRES 4G76 MSE A 3 MET SELENOMETHIONINE MODRES 4G76 MSE A 110 MET SELENOMETHIONINE MODRES 4G76 MSE A 159 MET SELENOMETHIONINE MODRES 4G76 MSE A 175 MET SELENOMETHIONINE MODRES 4G76 MSE A 187 MET SELENOMETHIONINE MODRES 4G76 MSE A 258 MET SELENOMETHIONINE HET MSE A 3 8 HET MSE A 110 8 HET MSE A 159 8 HET MSE A 175 8 HET MSE A 187 8 HET MSE A 258 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 HOH *112(H2 O) HELIX 1 1 GLY A 13 ASP A 16 5 4 HELIX 2 2 PHE A 17 ASN A 25 1 9 HELIX 3 3 GLY A 26 TRP A 29 5 4 HELIX 4 4 SER A 33 VAL A 50 1 18 HELIX 5 5 TRP A 54 ALA A 66 1 13 HELIX 6 6 PHE A 80 GLY A 103 1 24 HELIX 7 7 ASP A 105 GLN A 114 1 10 HELIX 8 8 TYR A 142 GLY A 154 1 13 HELIX 9 9 PRO A 162 ASN A 167 5 6 HELIX 10 10 ASN A 171 ALA A 174 5 4 HELIX 11 11 MSE A 175 SER A 185 1 11 HELIX 12 12 ALA A 201 ASP A 203 5 3 HELIX 13 13 SER A 204 ASN A 209 1 6 HELIX 14 14 ASN A 246 HIS A 250 5 5 HELIX 15 15 ARG A 251 GLU A 253 5 3 HELIX 16 16 THR A 254 VAL A 265 1 12 HELIX 17 17 GLY A 266 LYS A 268 5 3 SHEET 1 A 3 MSE A 159 ASN A 160 0 SHEET 2 A 3 TYR A 275 GLY A 278 1 O GLY A 278 N MSE A 159 SHEET 3 A 3 ASP A 241 TYR A 243 -1 N ASP A 241 O ILE A 277 SHEET 1 B 4 GLY A 188 ALA A 199 0 SHEET 2 B 4 GLU A 213 LYS A 224 -1 O LEU A 222 N THR A 190 SHEET 3 B 4 GLN A 229 ALA A 238 -1 O GLU A 235 N VAL A 219 SHEET 4 B 4 ILE A 283 ARG A 290 -1 O ILE A 283 N ILE A 236 LINK C MSE A 3 N ASP A 4 1555 1555 1.32 LINK C ALA A 109 N MSE A 110 1555 1555 1.33 LINK C MSE A 110 N ASN A 111 1555 1555 1.33 LINK C LYS A 158 N MSE A 159 1555 1555 1.33 LINK C MSE A 159 N ASN A 160 1555 1555 1.33 LINK C ALA A 174 N MSE A 175 1555 1555 1.33 LINK C MSE A 175 N PRO A 176 1555 1555 1.34 LINK C PRO A 186 N MSE A 187 1555 1555 1.33 LINK C MSE A 187 N GLY A 188 1555 1555 1.33 LINK C GLY A 257 N MSE A 258 1555 1555 1.33 LINK C MSE A 258 N THR A 259 1555 1555 1.33 CISPEP 1 ILE A 126 PRO A 127 0 -0.52 CRYST1 42.812 72.400 99.693 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 0.023358 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010031 0.00000