HEADER HYDROLASE 02-FEB-15 4XY5 TITLE CRYSTAL STRUCTURE OF MUTANT (ASP52ALA) HYPOTHETICAL THIOESTERASE TITLE 2 PROTEIN SP_1851 FROM STREPTOCOCCUS PNEUMONIAE TIGR4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL THIOESTERASE PROTEIN SP_1851; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE SEROTYPE 4 (STRAIN SOURCE 3 ATCC BAA-334 / TIGR4); SOURCE 4 ORGANISM_TAXID: 170187; SOURCE 5 STRAIN: ATCC BAA-334 / TIGR4; SOURCE 6 GENE: SP_1851; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG21 KEYWDS THIOESTERASE, STREPTOCOCCUS PNEUMONIAE, PAAI, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.B.KHANDOKAR,P.SRIVASTAVA,J.K.FORWOOD REVDAT 2 27-SEP-23 4XY5 1 SOURCE REMARK REVDAT 1 06-MAY-15 4XY5 0 JRNL AUTH Y.B.KHANDOKAR,P.SRIVASTAVA,J.K.FORWOOD JRNL TITL CRYSTAL STRUCTURE OF MUTANT (ASP52ALA) HYPOTHETICAL JRNL TITL 2 THIOESTERASE PROTEIN SP_1851 FROM STREPTOCOCCUS PNEUMONIAE JRNL TITL 3 TIGR4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 28.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 20832 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 : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1037 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 28.8879 - 3.4417 0.96 2853 134 0.1815 0.2127 REMARK 3 2 3.4417 - 2.7325 0.99 2842 163 0.1788 0.2404 REMARK 3 3 2.7325 - 2.3873 0.99 2849 150 0.1868 0.2318 REMARK 3 4 2.3873 - 2.1691 0.99 2818 157 0.1751 0.2103 REMARK 3 5 2.1691 - 2.0136 0.98 2829 148 0.1800 0.2428 REMARK 3 6 2.0136 - 1.8949 0.98 2825 126 0.1810 0.2486 REMARK 3 7 1.8949 - 1.8001 0.98 2779 159 0.1964 0.2774 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) : 23.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1872 REMARK 3 ANGLE : 0.997 2532 REMARK 3 CHIRALITY : 0.043 302 REMARK 3 PLANARITY : 0.004 322 REMARK 3 DIHEDRAL : 12.411 658 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 4XY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9196 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 31.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.08700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.60 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: 4I82 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, 100MM HEPES PH7.5, 200MM REMARK 280 MAGNESIUM CHLORIDE., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 17.90914 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.79700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.99588 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.90914 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.79700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 55.99588 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -18.37544 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 223.98351 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 279 LIES ON A SPECIAL POSITION. 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 -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASP A 3 REMARK 465 PHE A 4 REMARK 465 ARG A 126 REMARK 465 SER A 127 REMARK 465 GLU A 128 REMARK 465 GLU A 129 REMARK 465 ARG A 130 REMARK 465 ARG A 131 REMARK 465 VAL A 132 REMARK 465 ARG A 133 REMARK 465 ILE A 134 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 ASP B 3 REMARK 465 PHE B 4 REMARK 465 ARG B 126 REMARK 465 SER B 127 REMARK 465 GLU B 128 REMARK 465 GLU B 129 REMARK 465 ARG B 130 REMARK 465 ARG B 131 REMARK 465 VAL B 132 REMARK 465 ARG B 133 REMARK 465 ILE B 134 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 ASP A 82 -2.05 76.84 REMARK 500 PHE B 12 39.90 71.83 REMARK 500 ASP B 82 -0.22 76.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XY6 RELATED DB: PDB DBREF 4XY5 A 1 134 UNP Q97NZ8 Q97NZ8_STRPN 1 134 DBREF 4XY5 B 1 134 UNP Q97NZ8 Q97NZ8_STRPN 1 134 SEQADV 4XY5 SER A -2 UNP Q97NZ8 EXPRESSION TAG SEQADV 4XY5 ASN A -1 UNP Q97NZ8 EXPRESSION TAG SEQADV 4XY5 ALA A 0 UNP Q97NZ8 EXPRESSION TAG SEQADV 4XY5 ALA A 52 UNP Q97NZ8 ASP 52 ENGINEERED MUTATION SEQADV 4XY5 SER B -2 UNP Q97NZ8 EXPRESSION TAG SEQADV 4XY5 ASN B -1 UNP Q97NZ8 EXPRESSION TAG SEQADV 4XY5 ALA B 0 UNP Q97NZ8 EXPRESSION TAG SEQADV 4XY5 ALA B 52 UNP Q97NZ8 ASP 52 ENGINEERED MUTATION SEQRES 1 A 137 SER ASN ALA MET LYS ASP PHE HIS PHE ASP ALA ILE SER SEQRES 2 A 137 ALA PHE GLU ASN TYR GLU ILE GLU LYS MET ARG ASP GLY SEQRES 3 A 137 HIS VAL VAL VAL THR THR LYS VAL VAL ASN SER SER LEU SEQRES 4 A 137 ASN TYR TYR GLY ASN ALA HIS GLY GLY TYR LEU PHE THR SEQRES 5 A 137 LEU CYS ALA GLN ILE SER GLY LEU VAL VAL ILE SER LEU SEQRES 6 A 137 GLY LEU ASP GLY VAL THR LEU GLN SER SER ILE ASN TYR SEQRES 7 A 137 LEU LYS ALA GLY LYS LEU ASP ASP VAL LEU THR ILE LYS SEQRES 8 A 137 GLY GLU CYS VAL HIS GLN GLY ARG THR THR CYS VAL MET SEQRES 9 A 137 ASP VAL ASP ILE THR ASN GLN GLU GLY ARG ASN VAL CYS SEQRES 10 A 137 LYS ALA THR PHE THR MET PHE VAL THR GLY GLN ARG SER SEQRES 11 A 137 GLU GLU ARG ARG VAL ARG ILE SEQRES 1 B 137 SER ASN ALA MET LYS ASP PHE HIS PHE ASP ALA ILE SER SEQRES 2 B 137 ALA PHE GLU ASN TYR GLU ILE GLU LYS MET ARG ASP GLY SEQRES 3 B 137 HIS VAL VAL VAL THR THR LYS VAL VAL ASN SER SER LEU SEQRES 4 B 137 ASN TYR TYR GLY ASN ALA HIS GLY GLY TYR LEU PHE THR SEQRES 5 B 137 LEU CYS ALA GLN ILE SER GLY LEU VAL VAL ILE SER LEU SEQRES 6 B 137 GLY LEU ASP GLY VAL THR LEU GLN SER SER ILE ASN TYR SEQRES 7 B 137 LEU LYS ALA GLY LYS LEU ASP ASP VAL LEU THR ILE LYS SEQRES 8 B 137 GLY GLU CYS VAL HIS GLN GLY ARG THR THR CYS VAL MET SEQRES 9 B 137 ASP VAL ASP ILE THR ASN GLN GLU GLY ARG ASN VAL CYS SEQRES 10 B 137 LYS ALA THR PHE THR MET PHE VAL THR GLY GLN ARG SER SEQRES 11 B 137 GLU GLU ARG ARG VAL ARG ILE FORMUL 3 HOH *167(H2 O) HELIX 1 AA1 VAL A 32 LEU A 36 5 5 HELIX 2 AA2 HIS A 43 LEU A 62 1 20 HELIX 3 AA3 VAL B 32 LEU B 36 5 5 HELIX 4 AA4 HIS B 43 LEU B 62 1 20 SHEET 1 AA1 2 ILE A 9 ALA A 11 0 SHEET 2 AA1 2 ILE B 9 ALA B 11 -1 O ILE B 9 N ALA A 11 SHEET 1 AA212 GLU A 16 ARG A 21 0 SHEET 2 AA212 HIS A 24 LYS A 30 -1 O THR A 28 N GLU A 16 SHEET 3 AA212 VAL A 84 GLN A 94 -1 O ILE A 87 N VAL A 27 SHEET 4 AA212 THR A 98 THR A 106 -1 O THR A 106 N THR A 86 SHEET 5 AA212 ASN A 112 GLY A 124 -1 O VAL A 113 N ILE A 105 SHEET 6 AA212 ASP A 65 TYR A 75 -1 N VAL A 67 O PHE A 121 SHEET 7 AA212 ASP B 65 TYR B 75 -1 O SER B 71 N ILE A 73 SHEET 8 AA212 ASN B 112 GLY B 124 -1 O PHE B 121 N VAL B 67 SHEET 9 AA212 THR B 98 THR B 106 -1 N ILE B 105 O VAL B 113 SHEET 10 AA212 VAL B 84 GLN B 94 -1 N THR B 86 O THR B 106 SHEET 11 AA212 HIS B 24 LYS B 30 -1 N VAL B 27 O ILE B 87 SHEET 12 AA212 GLU B 16 ARG B 21 -1 N LYS B 19 O VAL B 26 CRYST1 45.006 45.594 112.368 90.00 94.69 90.00 I 1 2 1 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 0.022219 0.000000 0.001823 0.00000 SCALE2 0.000000 0.021932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008929 0.00000