HEADER HYDROLASE 09-SEP-21 7S57 TITLE STRUCTURE OF SORTASE A FROM STREPTOCOCCUS PYOGENES WITH THE B7-B8 LOOP TITLE 2 SEQUENCE OF ENTEROCOCCUS FAECALIS SORTASE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS A SORTASE, SORTASE A CHIMERA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SORTASE A,SORTASE PROTEIN SRTA,SORTASE A,SORTASE PROTEIN COMPND 5 SRTA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 GENE: SRTA, SRTA_1, SRTA_2, E0F66_05345, E0F67_00760, FGO82_09960, SOURCE 5 FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY31_04460, SOURCE 6 GQY92_04850, GTK43_04765, GTK52_04270, GTK53_04530, GTK54_03910, SOURCE 7 GUA39_04435, IB935_04675, IB936_04605, IB937_04535, IB938_05195, SOURCE 8 KUN2590_09100, KUN4944_08330, MGAS2221_0893, SAMEA1407055_00305, SOURCE 9 SAMEA1711644_00960, SAMEA3918953_00457, SPNIH34_10200, SOURCE 10 SPNIH35_09070, SORTASE A; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS SORTASE-FOLD, HYDROLASE, SORTASE, EIGHT-STRANDED BETA BARREL, KEYWDS 2 TRANSPEPTIDASE, HOUSEKEEPING SORTASE, SURFACE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.E.SVENDSEN,D.A.JOHNSON,M.GAO,J.M.ANTOS,J.F.AMACHER REVDAT 3 18-OCT-23 7S57 1 REMARK REVDAT 2 02-MAR-22 7S57 1 JRNL REVDAT 1 12-JAN-22 7S57 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. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15645 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 769 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 44.4950 - 2.9070 1.00 3103 183 0.1618 0.1943 REMARK 3 2 2.9070 - 2.3074 1.00 2989 146 0.1988 0.2693 REMARK 3 3 2.3074 - 2.0157 1.00 2956 144 0.1822 0.2005 REMARK 3 4 2.0157 - 1.8314 1.00 2909 158 0.1975 0.2401 REMARK 3 5 1.8314 - 1.7001 1.00 2919 138 0.2784 0.3475 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.36 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 : 0.007 1270 REMARK 3 ANGLE : 0.932 1725 REMARK 3 CHIRALITY : 0.055 198 REMARK 3 PLANARITY : 0.006 224 REMARK 3 DIHEDRAL : 6.911 1040 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 7S57 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_1000259516. 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 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 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: PHENIX REMARK 200 STARTING MODEL: 3FN5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 8000, 0.2 M SODIUM REMARK 280 ACETATE, 0.1 M TRIS PH 6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 16.79800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.67700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.45850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.67700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.79800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.45850 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 80 REMARK 465 SER A 81 REMARK 465 VAL A 82 REMARK 465 LEU A 83 REMARK 465 GLN A 84 REMARK 465 ALA A 85 REMARK 465 GLN A 86 REMARK 465 MET A 87 REMARK 465 ALA A 88 REMARK 465 ALA A 89 REMARK 465 GLN A 90 REMARK 465 GLN A 91 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 OE1 GLU A 102 O HOH A 301 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 313 O HOH A 382 4546 2.10 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 154 -124.62 50.81 REMARK 500 LYS A 172 -1.83 69.82 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7S57 A 81 208 UNP A0A4U7I1I9_STRPY DBREF2 7S57 A A0A4U7I1I9 81 208 DBREF 7S57 A 209 215 PDB 7S57 7S57 209 215 DBREF1 7S57 A 216 249 UNP A0A4U7I1I9_STRPY DBREF2 7S57 A A0A4U7I1I9 216 249 SEQADV 7S57 SER A 80 UNP A0A4U7I1I EXPRESSION TAG SEQRES 1 A 170 SER SER VAL LEU GLN ALA GLN MET ALA ALA GLN GLN LEU SEQRES 2 A 170 PRO VAL ILE GLY GLY ILE ALA ILE PRO GLU LEU GLY ILE SEQRES 3 A 170 ASN LEU PRO ILE PHE LYS GLY LEU GLY ASN THR GLU LEU SEQRES 4 A 170 ILE TYR GLY ALA GLY THR MET LYS GLU GLU GLN VAL MET SEQRES 5 A 170 GLY GLY GLU ASN ASN TYR SER LEU ALA SER HIS HIS ILE SEQRES 6 A 170 PHE GLY ILE THR GLY SER SER GLN MET LEU PHE SER PRO SEQRES 7 A 170 LEU GLU ARG ALA GLN ASN GLY MET SER ILE TYR LEU THR SEQRES 8 A 170 ASP LYS GLU LYS ILE TYR GLU TYR ILE ILE LYS ASP VAL SEQRES 9 A 170 PHE THR VAL ALA PRO GLU ARG VAL ASP VAL ILE ASP ASP SEQRES 10 A 170 THR ALA GLY LEU LYS GLU VAL THR LEU VAL THR CYS GLY SEQRES 11 A 170 ASP LEU GLN ALA THR THR ARG ILE ILE VAL LYS GLY GLU SEQRES 12 A 170 LEU LYS THR GLU TYR ASP PHE ASP LYS ALA PRO ALA ASP SEQRES 13 A 170 VAL LEU LYS ALA PHE ASN HIS SER TYR ASN GLN VAL SER SEQRES 14 A 170 THR FORMUL 2 HOH *107(H2 O) HELIX 1 AA1 PRO A 101 GLY A 104 5 4 HELIX 2 AA2 GLY A 114 GLY A 121 1 8 HELIX 3 AA3 GLY A 149 MET A 153 5 5 HELIX 4 AA4 PHE A 155 ALA A 161 5 7 HELIX 5 AA5 ARG A 190 ASP A 195 5 6 HELIX 6 AA6 ASP A 230 ALA A 232 5 3 HELIX 7 AA7 PRO A 233 HIS A 242 1 10 SHEET 1 AA1 9 VAL A 94 ILE A 100 0 SHEET 2 AA1 9 ILE A 105 PHE A 110 -1 O ILE A 105 N ILE A 100 SHEET 3 AA1 9 ALA A 122 THR A 124 1 O ALA A 122 N PHE A 110 SHEET 4 AA1 9 ASN A 136 ALA A 140 -1 O ALA A 140 N GLY A 123 SHEET 5 AA1 9 GLU A 202 CYS A 208 1 O THR A 204 N LEU A 139 SHEET 6 AA1 9 ARG A 216 ASP A 228 -1 O VAL A 219 N LEU A 205 SHEET 7 AA1 9 LYS A 174 VAL A 186 -1 N PHE A 184 O ILE A 218 SHEET 8 AA1 9 SER A 166 THR A 170 -1 N ILE A 167 O TYR A 178 SHEET 9 AA1 9 VAL A 94 ILE A 100 -1 N ALA A 99 O TYR A 168 CRYST1 33.596 56.917 71.354 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 0.029765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014015 0.00000