HEADER BIOSYNTHETIC PROTEIN 27-APR-20 6YV5 TITLE CRYSTAL STRUCTURE OF SERINE PROTEASE SPLB N3Q/S154R FROM TITLE 2 STAPHYLOCOCCUS AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SPLB PROTEASE; COMPND 5 EC: 3.4.21.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: SPLB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSF KEYWDS SPL, SERINE PROTEASE-LIKE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.R.RANGEL PEREIRA,P.BREAR,P.KNYPHAUSEN,L.JERMUTUS,F.HOLLFELDER REVDAT 3 31-JAN-24 6YV5 1 REMARK REVDAT 2 30-NOV-22 6YV5 1 TITLE JRNL REVDAT 1 12-MAY-21 6YV5 0 JRNL AUTH P.KNYPHAUSEN,M.R.RANGEL PEREIRA,P.BREAR,L.JERMUTUS, JRNL AUTH 2 F.HOLLFELDER JRNL TITL CRYSTAL STRUCTURE OF SERINE PROTEASE SPLB N3Q/S154R FROM JRNL TITL 2 STAPHYLOCOCCUS AUREUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 66027 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3296 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.69 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4069 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2303 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3849 REMARK 3 BIN R VALUE (WORKING SET) : 0.2299 REMARK 3 BIN FREE R VALUE : 0.2369 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.41 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 220 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1598 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35380 REMARK 3 B22 (A**2) : -0.76680 REMARK 3 B33 (A**2) : 0.41300 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.039 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.039 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.037 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.038 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1752 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2389 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 617 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 44 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 266 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1752 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 230 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2246 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.17 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 5.17 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.08 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 36.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.72600 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: PHASER REMARK 200 STARTING MODEL: 2VID REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350 30%, TRIS-CL PH 8.0, VAPOR REMARK 280 DIFFUSION, SITTING 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 17.46000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.57500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.57500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.46000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.17000 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 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 SER A 24 44.00 -146.08 REMARK 500 ALA A 25 -174.10 97.36 REMARK 500 ALA A 25 -174.10 170.00 REMARK 500 HIS A 54 57.95 33.36 REMARK 500 HIS A 54 57.26 29.07 REMARK 500 SER A 150 76.48 -107.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 24 O REMARK 620 2 SER A 24 OG 75.6 REMARK 620 3 TYR A 45 OH 66.6 72.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 301 DBREF1 6YV5 A 2 205 UNP A0A2D1PJH6_STAAU DBREF2 6YV5 A A0A2D1PJH6 9 212 SEQADV 6YV5 SER A 1 UNP A0A2D1PJH EXPRESSION TAG SEQADV 6YV5 GLN A 4 UNP A0A2D1PJH ASN 11 ENGINEERED MUTATION SEQADV 6YV5 ARG A 155 UNP A0A2D1PJH SER 162 ENGINEERED MUTATION SEQADV 6YV5 GLY A 206 UNP A0A2D1PJH EXPRESSION TAG SEQRES 1 A 206 SER GLU ASN GLN VAL THR LYS VAL LYS ASP THR ASN ILE SEQRES 2 A 206 PHE PRO TYR THR GLY VAL VAL ALA PHE LYS SER ALA THR SEQRES 3 A 206 GLY PHE VAL VAL GLY LYS ASN THR ILE LEU THR ASN LYS SEQRES 4 A 206 HIS VAL SER LYS ASN TYR LYS VAL GLY ASP ARG ILE THR SEQRES 5 A 206 ALA HIS PRO ASN SER ASP LYS GLY ASN GLY GLY ILE TYR SEQRES 6 A 206 SER ILE LYS LYS ILE ILE ASN TYR PRO GLY LYS GLU ASP SEQRES 7 A 206 VAL SER VAL ILE GLN VAL GLU GLU ARG ALA ILE GLU ARG SEQRES 8 A 206 GLY PRO LYS GLY PHE ASN PHE ASN ASP ASN VAL THR PRO SEQRES 9 A 206 PHE LYS TYR ALA ALA GLY ALA LYS ALA GLY GLU ARG ILE SEQRES 10 A 206 LYS VAL ILE GLY TYR PRO HIS PRO TYR LYS ASN LYS TYR SEQRES 11 A 206 VAL LEU TYR GLU SER THR GLY PRO VAL MET SER VAL GLU SEQRES 12 A 206 GLY SER SER ILE VAL TYR SER ALA HIS THR GLU ARG GLY SEQRES 13 A 206 ASN SER GLY SER PRO VAL LEU ASN SER ASN ASN GLU LEU SEQRES 14 A 206 VAL GLY ILE HIS PHE ALA SER ASP VAL LYS ASN ASP ASP SEQRES 15 A 206 ASN ARG ASN ALA TYR GLY VAL TYR PHE THR PRO GLU ILE SEQRES 16 A 206 LYS LYS PHE ILE ALA GLU ASN ILE ASP LYS GLY HET NA A 301 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *195(H2 O) HELIX 1 AA1 PRO A 15 THR A 17 5 3 HELIX 2 AA2 ASN A 38 LYS A 43 1 6 HELIX 3 AA3 PHE A 98 VAL A 102 1 5 HELIX 4 AA4 GLU A 154 SER A 158 5 5 HELIX 5 AA5 THR A 192 ASN A 202 1 11 SHEET 1 AA1 8 VAL A 5 LYS A 7 0 SHEET 2 AA1 8 TYR A 133 GLU A 143 -1 O GLU A 134 N THR A 6 SHEET 3 AA1 8 SER A 146 TYR A 149 -1 O VAL A 148 N MET A 140 SHEET 4 AA1 8 ALA A 186 VAL A 189 -1 O GLY A 188 N ILE A 147 SHEET 5 AA1 8 LEU A 169 SER A 176 -1 N ALA A 175 O TYR A 187 SHEET 6 AA1 8 PRO A 161 LEU A 163 -1 N VAL A 162 O VAL A 170 SHEET 7 AA1 8 ARG A 116 GLY A 121 -1 N LYS A 118 O LEU A 163 SHEET 8 AA1 8 TYR A 133 GLU A 143 -1 O SER A 135 N VAL A 119 SHEET 1 AA2 7 VAL A 19 ALA A 21 0 SHEET 2 AA2 7 THR A 26 GLY A 31 -1 O GLY A 27 N VAL A 20 SHEET 3 AA2 7 THR A 34 THR A 37 -1 O LEU A 36 N PHE A 28 SHEET 4 AA2 7 SER A 80 VAL A 84 -1 O ILE A 82 N ILE A 35 SHEET 5 AA2 7 ILE A 64 ASN A 72 -1 N ILE A 71 O VAL A 81 SHEET 6 AA2 7 ARG A 50 ALA A 53 -1 N ILE A 51 O TYR A 65 SHEET 7 AA2 7 VAL A 19 ALA A 21 -1 N ALA A 21 O THR A 52 SHEET 1 AA3 2 ARG A 87 GLY A 92 0 SHEET 2 AA3 2 GLY A 95 ASN A 97 -1 O PHE A 96 N ALA A 88 LINK O ASER A 24 NA NA A 301 1555 1555 2.47 LINK OG BSER A 24 NA NA A 301 1555 1555 2.72 LINK OH TYR A 45 NA NA A 301 1555 1555 2.99 CISPEP 1 PHE A 14 PRO A 15 0 8.16 SITE 1 AC1 3 SER A 24 ASN A 44 TYR A 45 CRYST1 34.920 64.340 73.150 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 0.028637 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015542 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013671 0.00000