HEADER TRANSFERASE 10-JUL-12 4G1H TITLE GROUP B STREPTOCOCCUS PILUS ISLAND 1 SORTASE C2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 19-233; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE SEROGROUP V; SOURCE 3 ORGANISM_TAXID: 216466; SOURCE 4 GENE: SAG0648; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYSTEINE PROTEASE, EXTRACELLULAR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.COZZI,D.M.PRIGOZHIN,T.ALBER REVDAT 2 28-FEB-24 4G1H 1 REMARK REVDAT 1 05-DEC-12 4G1H 0 JRNL AUTH R.COZZI,D.PRIGOZHIN,R.ROSINI,F.ABATE,M.J.BOTTOMLEY,G.GRANDI, JRNL AUTH 2 J.L.TELFORD,C.D.RINAUDO,D.MAIONE,T.ALBER JRNL TITL STRUCTURAL BASIS FOR GROUP B STREPTOCOCCUS PILUS 1 SORTASES JRNL TITL 2 C REGULATION AND SPECIFICITY. JRNL REF PLOS ONE V. 7 49048 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 23145064 JRNL DOI 10.1371/JOURNAL.PONE.0049048 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 17187 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1716 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 30.2200 - 3.8770 0.99 1759 196 0.1827 0.2003 REMARK 3 2 3.8770 - 3.0782 1.00 1668 185 0.2015 0.2372 REMARK 3 3 3.0782 - 2.6894 1.00 1642 182 0.2373 0.2761 REMARK 3 4 2.6894 - 2.4436 0.99 1622 179 0.2291 0.3073 REMARK 3 5 2.4436 - 2.2685 0.98 1589 180 0.2191 0.2640 REMARK 3 6 2.2685 - 2.1348 0.98 1571 174 0.2241 0.2930 REMARK 3 7 2.1348 - 2.0279 0.95 1535 168 0.2292 0.2729 REMARK 3 8 2.0279 - 1.9397 0.92 1477 160 0.2345 0.2910 REMARK 3 9 1.9397 - 1.8650 0.88 1411 159 0.2541 0.2945 REMARK 3 10 1.8650 - 1.8000 0.75 1197 133 0.2945 0.3241 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 : 0.34 REMARK 3 B_SOL : 39.64 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.17350 REMARK 3 B22 (A**2) : -5.17350 REMARK 3 B33 (A**2) : 10.34700 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 : 0.007 1393 REMARK 3 ANGLE : 1.088 1894 REMARK 3 CHIRALITY : 0.070 233 REMARK 3 PLANARITY : 0.004 237 REMARK 3 DIHEDRAL : 11.595 521 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 4G1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073618. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115889 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.12100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.21750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.21750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.56050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.21750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.21750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.68150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.21750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.21750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.56050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.21750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.21750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.68150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.12100 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 ALA A 42 REMARK 465 SER A 43 REMARK 465 HIS A 44 REMARK 465 GLN A 45 REMARK 465 ASN A 46 REMARK 465 ILE A 47 REMARK 465 ASN A 48 REMARK 465 GLN A 49 REMARK 465 PHE A 50 REMARK 465 LYS A 51 REMARK 465 ARG A 52 REMARK 465 GLU A 53 REMARK 465 VAL A 54 REMARK 465 ALA A 55 REMARK 465 LYS A 56 REMARK 465 GLN A 90 REMARK 465 LYS A 91 REMARK 465 GLU A 92 REMARK 465 GLY A 93 REMARK 465 TYR A 237 REMARK 465 ASP A 238 REMARK 465 SER A 239 REMARK 465 THR A 240 REMARK 465 GLU A 241 REMARK 465 ALA A 242 REMARK 465 GLU A 243 REMARK 465 LYS A 244 REMARK 465 HIS A 245 REMARK 465 LYS A 246 REMARK 465 GLU A 247 REMARK 465 GLN A 248 REMARK 465 THR A 249 REMARK 465 VAL A 250 REMARK 465 GLN A 251 REMARK 465 ASP A 252 REMARK 465 TYR A 253 REMARK 465 ARG A 254 REMARK 465 LEU A 255 REMARK 465 SER A 256 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OH TYR A 178 OH TYR A 178 8665 1.97 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 GLU A 105 -0.12 72.63 REMARK 500 LEU A 164 -122.62 45.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G1J RELATED DB: PDB DBREF 4G1H A 42 256 UNP Q8E0S6 Q8E0S6_STRA5 19 233 SEQRES 1 A 215 ALA SER HIS GLN ASN ILE ASN GLN PHE LYS ARG GLU VAL SEQRES 2 A 215 ALA LYS ILE ASP THR ASN THR VAL GLU ARG ARG ILE ALA SEQRES 3 A 215 LEU ALA ASN ALA TYR ASN GLU THR LEU SER ARG ASN PRO SEQRES 4 A 215 LEU LEU ILE ASP PRO PHE THR SER LYS GLN LYS GLU GLY SEQRES 5 A 215 LEU ARG GLU TYR ALA ARG MET LEU GLU VAL HIS GLU GLN SEQRES 6 A 215 ILE GLY HIS VAL ALA ILE PRO SER ILE GLY VAL ASP ILE SEQRES 7 A 215 PRO ILE TYR ALA GLY THR SER GLU THR VAL LEU GLN LYS SEQRES 8 A 215 GLY SER GLY HIS LEU GLU GLY THR SER LEU PRO VAL GLY SEQRES 9 A 215 GLY LEU SER THR HIS SER VAL LEU THR ALA HIS ARG GLY SEQRES 10 A 215 LEU PRO THR ALA ARG LEU PHE THR ASP LEU ASN LYS VAL SEQRES 11 A 215 LYS LYS GLY GLN ILE PHE TYR VAL THR ASN ILE LYS GLU SEQRES 12 A 215 THR LEU ALA TYR LYS VAL VAL SER ILE LYS VAL VAL ASP SEQRES 13 A 215 PRO THR ALA LEU SER GLU VAL LYS ILE VAL ASN GLY LYS SEQRES 14 A 215 ASP TYR ILE THR LEU LEU THR CYS THR PRO TYR MET ILE SEQRES 15 A 215 ASN SER HIS ARG LEU LEU VAL LYS GLY GLU ARG ILE PRO SEQRES 16 A 215 TYR ASP SER THR GLU ALA GLU LYS HIS LYS GLU GLN THR SEQRES 17 A 215 VAL GLN ASP TYR ARG LEU SER HET CA A 301 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *91(H2 O) HELIX 1 1 ASP A 58 GLU A 74 1 17 HELIX 2 2 ALA A 98 GLU A 102 5 5 HELIX 3 3 PRO A 113 GLY A 116 5 4 HELIX 4 4 SER A 126 GLY A 133 1 8 HELIX 5 5 ASP A 167 VAL A 171 5 5 HELIX 6 6 ASP A 197 VAL A 204 5 8 SHEET 1 A 9 GLY A 108 ILE A 112 0 SHEET 2 A 9 VAL A 117 ALA A 123 -1 O ILE A 121 N GLY A 108 SHEET 3 A 9 SER A 134 HIS A 136 1 O SER A 134 N PRO A 120 SHEET 4 A 9 THR A 149 THR A 154 -1 O THR A 154 N GLY A 135 SHEET 5 A 9 ASP A 211 THR A 219 1 O LEU A 216 N LEU A 153 SHEET 6 A 9 HIS A 226 ARG A 234 -1 O HIS A 226 N THR A 219 SHEET 7 A 9 THR A 185 VAL A 196 -1 N LYS A 194 O LEU A 229 SHEET 8 A 9 ILE A 176 THR A 180 -1 N VAL A 179 O LEU A 186 SHEET 9 A 9 GLY A 108 ILE A 112 -1 N ALA A 111 O TYR A 178 LINK CA CA A 301 O HOH A 421 1555 1555 3.14 CISPEP 1 THR A 219 PRO A 220 0 -6.81 SITE 1 AC1 3 ARG A 95 GLU A 96 TYR A 97 CRYST1 60.435 60.435 102.242 90.00 90.00 90.00 P 41 21 2 8 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 0.016547 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009781 0.00000