HEADER HYDROLASE 30-JUL-19 6PYM TITLE STRUCTURE OF ACTIVE-SITE SERINE MUTANT OF ESP, SERINE PROTEASE FROM TITLE 2 STAPHYLOCOCCUS EPIDERMIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMYL ENDOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUTAMIC ACID-SPECIFIC PROTEASE,GLUSE; COMPND 5 EC: 3.4.21.19; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS EPIDERMIDIS (STRAIN ATCC 12228); SOURCE 3 ORGANISM_TAXID: 176280; SOURCE 4 STRAIN: ATCC 12228; SOURCE 5 ATCC: 12228; SOURCE 6 GENE: GSEA, ESP, SE_1543; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SERINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.MANNE,S.V.L.NARAYANA REVDAT 4 11-OCT-23 6PYM 1 REMARK REVDAT 3 08-JAN-20 6PYM 1 JRNL REVDAT 2 18-DEC-19 6PYM 1 REMARK REVDAT 1 14-AUG-19 6PYM 0 JRNL AUTH K.MANNE,S.V.L.NARAYANA JRNL TITL STRUCTURAL INSIGHTS INTO THE ROLE OF THE N-TERMINUS IN THE JRNL TITL 2 ACTIVATION AND FUNCTION OF EXTRACELLULAR SERINE PROTEASE JRNL TITL 3 FROM STAPHYLOCOCCUS EPIDERMIDIS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 76 28 2020 JRNL REFN ESSN 1399-0047 JRNL DOI 10.1107/S2059798319015055 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.386 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 118240 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.964 REMARK 3 FREE R VALUE TEST SET COUNT : 3505 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 39.1693 - 3.5081 0.76 3650 112 0.1768 0.1637 REMARK 3 2 3.5081 - 2.7847 0.95 4560 138 0.1546 0.1637 REMARK 3 3 2.7847 - 2.4327 0.99 4698 149 0.1696 0.1903 REMARK 3 4 2.4327 - 2.2103 0.99 4692 136 0.1596 0.1533 REMARK 3 5 2.2103 - 2.0519 0.99 4775 150 0.1470 0.1348 REMARK 3 6 2.0519 - 1.9309 0.94 4505 137 0.1502 0.1356 REMARK 3 7 1.9309 - 1.8342 0.97 4631 128 0.1529 0.1642 REMARK 3 8 1.8342 - 1.7544 0.97 4655 158 0.1536 0.1760 REMARK 3 9 1.7544 - 1.6869 0.99 4696 131 0.1528 0.1449 REMARK 3 10 1.6869 - 1.6287 0.98 4741 141 0.1474 0.1933 REMARK 3 11 1.6287 - 1.5777 0.99 4679 142 0.1584 0.1865 REMARK 3 12 1.5777 - 1.5326 0.99 4750 149 0.1559 0.1751 REMARK 3 13 1.5326 - 1.4923 0.99 4727 153 0.1550 0.1830 REMARK 3 14 1.4923 - 1.4559 0.96 4569 143 0.1523 0.1287 REMARK 3 15 1.4559 - 1.4228 0.97 4668 132 0.1538 0.1854 REMARK 3 16 1.4228 - 1.3925 0.98 4732 160 0.1543 0.1641 REMARK 3 17 1.3925 - 1.3646 0.98 4646 143 0.1531 0.1723 REMARK 3 18 1.3646 - 1.3389 0.98 4697 144 0.1614 0.1534 REMARK 3 19 1.3389 - 1.3150 0.98 4700 135 0.1600 0.1868 REMARK 3 20 1.3150 - 1.2927 0.98 4674 148 0.1552 0.1538 REMARK 3 21 1.2927 - 1.2718 0.99 4688 141 0.1635 0.1659 REMARK 3 22 1.2718 - 1.2523 0.98 4711 133 0.1636 0.1842 REMARK 3 23 1.2523 - 1.2338 0.97 4657 154 0.1687 0.1820 REMARK 3 24 1.2338 - 1.2165 0.90 4267 142 0.1722 0.1817 REMARK 3 25 1.2430 - 1.2000 0.82 3967 106 0.1677 0.1936 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.069 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.20 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 : 0.004 1683 REMARK 3 ANGLE : 0.825 2293 REMARK 3 CHIRALITY : 0.091 250 REMARK 3 PLANARITY : 0.006 310 REMARK 3 DIHEDRAL : 13.476 612 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 6PYM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243223. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-18 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119842 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 39.169 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.01531 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 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: PHENIX REMARK 200 STARTING MODEL: 4JCN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.1M HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING 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 30.51300 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 ILE A 95 REMARK 465 ASP A 96 REMARK 465 GLY A 97 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 ASN A 192 -3.78 81.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 6PYM A 67 282 UNP P0C0Q2 GSEA_STAES 67 282 SEQADV 6PYM ALA A 235 UNP P0C0Q2 SER 235 ENGINEERED MUTATION SEQRES 1 A 216 VAL ILE LEU PRO ASN ASN ASN ARG HIS GLN ILE PHE ASN SEQRES 2 A 216 THR THR GLN GLY HIS TYR ASP ALA VAL SER PHE ILE TYR SEQRES 3 A 216 ILE PRO ILE ASP GLY GLY TYR MET SER GLY SER GLY VAL SEQRES 4 A 216 VAL VAL GLY GLU ASN GLU ILE LEU THR ASN LYS HIS VAL SEQRES 5 A 216 VAL ASN GLY ALA LYS GLY ASN PRO ARG ASN ILE SER VAL SEQRES 6 A 216 HIS PRO SER ALA LYS ASN GLU ASN ASP TYR PRO ASN GLY SEQRES 7 A 216 LYS PHE VAL GLY GLN GLU ILE ILE PRO TYR PRO GLY ASN SEQRES 8 A 216 SER ASP LEU ALA ILE LEU ARG VAL SER PRO ASN GLU HIS SEQRES 9 A 216 ASN GLN HIS ILE GLY GLN VAL VAL LYS PRO ALA THR ILE SEQRES 10 A 216 SER SER ASN THR ASP THR ARG ILE ASN GLU ASN ILE THR SEQRES 11 A 216 VAL THR GLY TYR PRO GLY ASP LYS PRO LEU ALA THR MET SEQRES 12 A 216 TRP GLU SER VAL GLY LYS VAL VAL TYR ILE GLY GLY GLU SEQRES 13 A 216 GLU LEU ARG TYR ASP LEU SER THR VAL GLY GLY ASN ALA SEQRES 14 A 216 GLY SER PRO VAL PHE ASN GLY LYS ASN GLN VAL ILE GLY SEQRES 15 A 216 ILE HIS TYR GLY GLY VAL ASP ASN LYS TYR ASN SER SER SEQRES 16 A 216 VAL TYR ILE ASN ASP PHE VAL GLN GLN PHE LEU ARG ASN SEQRES 17 A 216 ASN ILE PRO ASP ILE ASN ILE GLN FORMUL 2 HOH *299(H2 O) HELIX 1 AA1 GLN A 82 ASP A 86 5 5 HELIX 2 AA2 ASN A 115 ASN A 120 1 6 HELIX 3 AA3 GLY A 121 LYS A 123 5 3 HELIX 4 AA4 ASN A 125 ASN A 128 5 4 HELIX 5 AA5 HIS A 173 VAL A 178 1 6 HELIX 6 AA6 ASN A 265 ILE A 276 1 12 SHEET 1 AA1 8 ARG A 74 ILE A 77 0 SHEET 2 AA1 8 MET A 209 GLY A 220 -1 O MET A 209 N ILE A 77 SHEET 3 AA1 8 GLU A 223 TYR A 226 -1 O ARG A 225 N VAL A 217 SHEET 4 AA1 8 TYR A 258 TYR A 263 -1 O SER A 261 N LEU A 224 SHEET 5 AA1 8 VAL A 246 VAL A 254 -1 N GLY A 252 O SER A 260 SHEET 6 AA1 8 PRO A 238 PHE A 240 -1 N VAL A 239 O ILE A 247 SHEET 7 AA1 8 ASN A 194 GLY A 199 -1 N THR A 196 O PHE A 240 SHEET 8 AA1 8 MET A 209 GLY A 220 -1 O GLY A 214 N ILE A 195 SHEET 1 AA2 7 VAL A 88 ILE A 93 0 SHEET 2 AA2 7 MET A 100 GLY A 108 -1 O GLY A 104 N SER A 89 SHEET 3 AA2 7 GLU A 111 THR A 114 -1 O GLU A 111 N VAL A 107 SHEET 4 AA2 7 ALA A 161 VAL A 165 -1 O ALA A 161 N THR A 114 SHEET 5 AA2 7 PHE A 146 PRO A 153 -1 N GLN A 149 O ARG A 164 SHEET 6 AA2 7 SER A 130 PRO A 133 -1 N VAL A 131 O PHE A 146 SHEET 7 AA2 7 VAL A 88 ILE A 93 -1 N PHE A 90 O HIS A 132 CRYST1 39.621 61.026 42.512 90.00 98.66 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 0.025239 0.000000 0.003844 0.00000 SCALE2 0.000000 0.016386 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023794 0.00000