HEADER HYDROLASE 09-SEP-21 7S56 TITLE SORTASE A FROM STREPTOCOCCUS AGALACTIAE, RESIDUES 79-247 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS A SORTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 79-247; COMPND 5 SYNONYM: SORTASE,SORTASE A,LPXTG SPECIFIC,SRTA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE; SOURCE 3 ORGANISM_TAXID: 1311; SOURCE 4 GENE: SRTA, C4618_06055, F5043_06280, GD434_06060, NCTC6175_01342, SOURCE 5 RDF_0944; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS SORTASE-FOLD, HYDROLASE, SORTASE, EIGHT-STANDED BETA BARREL, KEYWDS 2 TRANSPEPTIDASE, HOUSEKEEPING SORTASE, SURFACE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.GAO,H.M.KODAMA,J.M.ANTOS,J.F.AMACHER REVDAT 3 18-OCT-23 7S56 1 REMARK REVDAT 2 02-MAR-22 7S56 1 JRNL REVDAT 1 12-JAN-22 7S56 0 JRNL AUTH M.GAO,D.A.JOHNSON,I.M.PIPER,H.M.KODAMA,J.E.SVENDSEN,E.TAHTI, JRNL AUTH 2 F.LONGSHORE-NEATE,B.VOGEL,J.M.ANTOS,J.F.AMACHER JRNL TITL STRUCTURAL AND BIOCHEMICAL ANALYSES OF SELECTIVITY JRNL TITL 2 DETERMINANTS IN CHIMERIC STREPTOCOCCUS CLASS A SORTASE JRNL TITL 3 ENZYMES. JRNL REF PROTEIN SCI. V. 31 701 2022 JRNL REFN ESSN 1469-896X JRNL PMID 34939250 JRNL DOI 10.1002/PRO.4266 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 29340 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1463 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 10.0000 - 3.0100 1.00 2970 152 0.1575 0.1575 REMARK 3 2 3.0100 - 2.3900 1.00 2839 151 0.1714 0.2078 REMARK 3 3 2.3900 - 2.0900 0.99 2778 178 0.1673 0.2067 REMARK 3 4 2.0900 - 1.9000 1.00 2775 146 0.1620 0.1859 REMARK 3 5 1.9000 - 1.7600 1.00 2776 134 0.2057 0.2289 REMARK 3 6 1.7600 - 1.6600 1.00 2770 153 0.1833 0.2116 REMARK 3 7 1.6600 - 1.5700 1.00 2754 142 0.2003 0.2135 REMARK 3 8 1.5700 - 1.5100 1.00 2767 148 0.2979 0.3660 REMARK 3 9 1.5100 - 1.4500 1.00 2770 126 0.3389 0.3668 REMARK 3 10 1.4500 - 1.4000 0.97 2678 133 0.3206 0.3417 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.53 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 : 0.010 1303 REMARK 3 ANGLE : 1.102 1765 REMARK 3 CHIRALITY : 0.089 206 REMARK 3 PLANARITY : 0.007 224 REMARK 3 DIHEDRAL : 6.244 174 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 7S56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977410 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29340 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 29.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 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) : 0.69400 REMARK 200 FOR SHELL : 3.780 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3RCC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (V/V) 2-PROPANOL, 0.1 M MES REMARK 280 MONOHYDRATE PH 6.1, 20% (W/V) PEG MONOMETHYL ETHER 2000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 22.06700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.12300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.31750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.12300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.06700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.31750 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 SER A 79 REMARK 465 ILE A 80 REMARK 465 LEU A 81 REMARK 465 SER A 82 REMARK 465 ALA A 83 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 OE2 GLU A 187 O HOH A 301 1.96 REMARK 500 O HOH A 360 O HOH A 429 1.98 REMARK 500 O HOH A 448 O HOH A 504 1.99 REMARK 500 O HOH A 463 O HOH A 505 2.04 REMARK 500 O HOH A 353 O HOH A 415 2.14 REMARK 500 O HOH A 445 O HOH A 472 2.17 REMARK 500 O HOH A 456 O HOH A 464 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 453 O HOH A 461 3445 2.00 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 LEU A 152 -130.25 56.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 506 DISTANCE = 6.63 ANGSTROMS DBREF1 7S56 A 79 247 UNP A0A0H1I052_STRAG DBREF2 7S56 A A0A0H1I052 79 247 SEQRES 1 A 169 SER ILE LEU SER ALA GLN THR LYS SER HIS ASN LEU PRO SEQRES 2 A 169 VAL ILE GLY GLY ILE ALA ILE PRO ASP VAL GLU ILE ASN SEQRES 3 A 169 LEU PRO ILE PHE LYS GLY LEU GLY ASN THR GLU LEU SER SEQRES 4 A 169 TYR GLY ALA GLY THR MET LYS GLU ASN GLN ILE MET GLY SEQRES 5 A 169 GLY PRO ASN ASN TYR ALA LEU ALA SER HIS HIS VAL PHE SEQRES 6 A 169 GLY LEU THR GLY SER SER LYS MET LEU PHE SER PRO LEU SEQRES 7 A 169 GLU HIS ALA LYS LYS GLY MET LYS VAL TYR LEU THR ASP SEQRES 8 A 169 LYS SER LYS VAL TYR THR TYR THR ILE THR GLU ILE SER SEQRES 9 A 169 LYS VAL THR PRO GLU HIS VAL GLU VAL ILE ASP ASP THR SEQRES 10 A 169 PRO GLY LYS SER GLN LEU THR LEU VAL THR CYS THR ASP SEQRES 11 A 169 PRO GLU ALA THR GLU ARG ILE ILE VAL HIS ALA GLU LEU SEQRES 12 A 169 GLU LYS THR GLY GLU PHE SER THR ALA ASP GLU SER ILE SEQRES 13 A 169 LEU LYS ALA PHE SER LYS LYS TYR ASN GLN ILE ASN LEU FORMUL 2 HOH *206(H2 O) HELIX 1 AA1 PRO A 99 GLU A 102 5 4 HELIX 2 AA2 GLY A 112 GLY A 119 1 8 HELIX 3 AA3 GLY A 147 MET A 151 5 5 HELIX 4 AA4 PHE A 153 ALA A 159 5 7 HELIX 5 AA5 HIS A 188 ASP A 193 5 6 HELIX 6 AA6 SER A 228 ALA A 230 5 3 HELIX 7 AA7 ASP A 231 LYS A 240 1 10 SHEET 1 AA1 2 LYS A 86 SER A 87 0 SHEET 2 AA1 2 LEU A 90 PRO A 91 -1 O LEU A 90 N SER A 87 SHEET 1 AA2 9 GLY A 94 ILE A 98 0 SHEET 2 AA2 9 ILE A 103 PHE A 108 -1 O LEU A 105 N ILE A 96 SHEET 3 AA2 9 ALA A 120 THR A 122 1 O ALA A 120 N PHE A 108 SHEET 4 AA2 9 ASN A 134 ALA A 138 -1 O ALA A 138 N GLY A 121 SHEET 5 AA2 9 GLN A 200 CYS A 206 1 O THR A 202 N LEU A 137 SHEET 6 AA2 9 ARG A 214 GLU A 226 -1 O ALA A 219 N LEU A 201 SHEET 7 AA2 9 LYS A 172 VAL A 184 -1 N THR A 175 O GLU A 222 SHEET 8 AA2 9 LYS A 164 THR A 168 -1 N VAL A 165 O TYR A 176 SHEET 9 AA2 9 GLY A 94 ILE A 98 -1 N ALA A 97 O TYR A 166 CRYST1 44.134 54.635 60.246 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 0.022658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018303 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016599 0.00000