HEADER TRANSFERASE , HYDROLASE 19-JUL-10 3O0P TITLE PILUS-RELATED SORTASE C OF GROUP B STREPTOCOCCUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE; SOURCE 3 ORGANISM_TAXID: 342614; SOURCE 4 STRAIN: STRAIN 515 (SEROTYPE IA); SOURCE 5 GENE: PILUS ISLAND 2A (PI-2A), SAL_1484; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET 54 DEST KEYWDS SORTASE, PILI ASSEMBLY, PILI SUBUNITS, TRANSFERASE ,HYDROLASE, KEYWDS 2 TRANSFERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.MALITO,G.SPRAGGON REVDAT 2 17-AUG-11 3O0P 1 JRNL VERSN REVDAT 1 09-MAR-11 3O0P 0 JRNL AUTH R.COZZI,E.MALITO,A.NUCCITELLI,M.D'ONOFRIO,M.MARTINELLI, JRNL AUTH 2 I.FERLENGHI,G.GRANDI,J.L.TELFORD,D.MAIONE,C.D.RINAUDO JRNL TITL STRUCTURE ANALYSIS AND SITE-DIRECTED MUTAGENESIS OF DEFINED JRNL TITL 2 KEY RESIDUES AND MOTIVES FOR PILUS-RELATED SORTASE C1 IN JRNL TITL 3 GROUP B STREPTOCOCCUS. JRNL REF FASEB J. V. 25 1874 2011 JRNL REFN ISSN 0892-6638 JRNL PMID 21357525 JRNL DOI 10.1096/FJ.10-174797 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 39285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1988 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 44.8078 - 3.1205 1.00 2955 173 0.1757 0.1789 REMARK 3 2 3.1205 - 2.4769 1.00 2910 146 0.1702 0.1914 REMARK 3 3 2.4769 - 2.1638 1.00 2887 169 0.1562 0.1869 REMARK 3 4 2.1638 - 1.9659 1.00 2875 144 0.1434 0.1690 REMARK 3 5 1.9659 - 1.8250 1.00 2862 155 0.1389 0.1845 REMARK 3 6 1.8250 - 1.7174 0.99 2823 167 0.1360 0.1708 REMARK 3 7 1.7174 - 1.6314 0.99 2813 189 0.1255 0.1633 REMARK 3 8 1.6314 - 1.5604 0.98 2821 132 0.1248 0.1794 REMARK 3 9 1.5604 - 1.5003 0.97 2773 145 0.1237 0.1735 REMARK 3 10 1.5003 - 1.4485 0.96 2762 148 0.1261 0.1524 REMARK 3 11 1.4485 - 1.4032 0.91 2617 129 0.1263 0.1705 REMARK 3 12 1.4032 - 1.3631 0.86 2455 108 0.1310 0.1991 REMARK 3 13 1.3631 - 1.3272 0.75 2170 100 0.1445 0.1765 REMARK 3 14 1.3272 - 1.2949 0.55 1574 83 0.1659 0.2193 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 : 0.40 REMARK 3 B_SOL : 59.71 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.11550 REMARK 3 B22 (A**2) : 4.55780 REMARK 3 B33 (A**2) : -3.44240 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.20110 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 : 0.010 1511 REMARK 3 ANGLE : 1.279 2052 REMARK 3 CHIRALITY : 0.071 240 REMARK 3 PLANARITY : 0.008 264 REMARK 3 DIHEDRAL : 14.971 547 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 3O0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-10. REMARK 100 THE RCSB ID CODE IS RCSB060517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9765 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40390 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 38.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41200 REMARK 200 FOR SHELL : 3.000 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: PDB ENTRY 2W1J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS, 200MM NAOAC, 30% PEG-4000, REMARK 280 PH 8.5, VAPOR DIFFUSION, 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 18.67700 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 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 GLY A 39 REMARK 465 SER A 40 REMARK 465 PHE A 41 REMARK 465 THR A 42 REMARK 465 GLU A 43 REMARK 465 SER A 44 REMARK 465 ASN A 45 REMARK 465 ASN A 46 REMARK 465 GLN A 92 REMARK 465 LYS A 93 REMARK 465 GLY A 240 REMARK 465 PRO A 241 REMARK 465 ILE A 242 REMARK 465 ASP A 243 REMARK 465 GLU A 244 REMARK 465 LYS A 245 REMARK 465 LEU A 246 REMARK 465 ILE A 247 REMARK 465 LYS A 248 REMARK 465 ASP A 249 REMARK 465 ASN A 253 REMARK 465 THR A 254 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 47 CG CD OE1 NE2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 VAL A 80 CG1 CG2 REMARK 470 HIS A 81 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 87 CG CD OE1 OE2 REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 91 CG1 CG2 CD1 REMARK 470 GLN A 128 CG CD OE1 NE2 REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 LYS A 163 CG CD CE NZ REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 LYS A 239 CG CD CE NZ 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 LEU A 165 -125.32 48.37 REMARK 500 MET A 223 -3.73 72.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 3O0P A 42 253 UNP Q3DMP3 Q3DMP3_STRAG 42 253 SEQADV 3O0P GLY A 39 UNP Q3DMP3 EXPRESSION TAG SEQADV 3O0P SER A 40 UNP Q3DMP3 EXPRESSION TAG SEQADV 3O0P PHE A 41 UNP Q3DMP3 EXPRESSION TAG SEQADV 3O0P THR A 42 UNP Q3DMP3 EXPRESSION TAG SEQRES 1 A 216 GLY SER PHE THR GLU SER ASN ASN GLN THR GLN ASP PHE SEQRES 2 A 216 GLU ARG ALA ALA LYS LYS LEU SER GLN LYS GLU ILE ASN SEQRES 3 A 216 ARG ARG MET ALA LEU ALA GLN ALA TYR ASN ASP SER LEU SEQRES 4 A 216 ASN ASN VAL HIS LEU GLU ASP PRO TYR GLU LYS LYS ARG SEQRES 5 A 216 ILE GLN LYS GLY ILE ALA GLU TYR ALA ARG MET LEU GLU SEQRES 6 A 216 VAL SER GLU LYS ILE GLY ILE ILE SER VAL PRO LYS ILE SEQRES 7 A 216 GLY GLN LYS LEU PRO ILE PHE ALA GLY SER SER GLN GLU SEQRES 8 A 216 VAL LEU SER LYS GLY ALA GLY HIS LEU GLU GLY THR SER SEQRES 9 A 216 LEU PRO ILE GLY GLY ASN SER THR HIS THR VAL ILE THR SEQRES 10 A 216 ALA HIS SER GLY ILE PRO ASP LYS GLU LEU PHE SER ASN SEQRES 11 A 216 LEU LYS LYS LEU LYS LYS GLY ASP LYS PHE TYR ILE GLN SEQRES 12 A 216 ASN ILE LYS GLU THR ILE ALA TYR GLN VAL ASP GLN ILE SEQRES 13 A 216 LYS VAL VAL THR PRO ASP ASN PHE SER ASP LEU LEU VAL SEQRES 14 A 216 VAL PRO GLY HIS ASP TYR ALA THR LEU LEU THR CYS THR SEQRES 15 A 216 PRO ILE MET VAL ASN THR HIS ARG LEU LEU VAL ARG GLY SEQRES 16 A 216 HIS ARG ILE PRO TYR LYS GLY PRO ILE ASP GLU LYS LEU SEQRES 17 A 216 ILE LYS ASP GLY HIS LEU ASN THR FORMUL 2 HOH *173(H2 O) HELIX 1 1 THR A 48 LYS A 57 1 10 HELIX 2 2 SER A 59 SER A 76 1 18 HELIX 3 3 ASN A 78 LEU A 82 5 5 HELIX 4 4 ALA A 99 GLU A 103 5 5 HELIX 5 5 PRO A 114 GLY A 117 5 4 HELIX 6 6 SER A 127 SER A 132 1 6 HELIX 7 7 ASN A 168 LEU A 172 5 5 HELIX 8 8 PHE A 202 LEU A 206 5 5 SHEET 1 A 9 GLY A 109 VAL A 113 0 SHEET 2 A 9 GLN A 118 PHE A 123 -1 O ILE A 122 N GLY A 109 SHEET 3 A 9 ALA A 135 HIS A 137 1 O ALA A 135 N PRO A 121 SHEET 4 A 9 THR A 150 THR A 155 -1 O THR A 155 N GLY A 136 SHEET 5 A 9 ASP A 212 THR A 220 1 O TYR A 213 N THR A 150 SHEET 6 A 9 HIS A 227 ILE A 236 -1 O HIS A 227 N THR A 220 SHEET 7 A 9 THR A 186 VAL A 197 -1 N LYS A 195 O LEU A 230 SHEET 8 A 9 LYS A 177 GLN A 181 -1 N ILE A 180 O ILE A 187 SHEET 9 A 9 GLY A 109 VAL A 113 -1 N SER A 112 O TYR A 179 CISPEP 1 THR A 220 PRO A 221 0 -10.43 CRYST1 45.087 37.354 51.242 90.00 96.68 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 0.022179 0.000000 0.002598 0.00000 SCALE2 0.000000 0.026771 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019649 0.00000