HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 07-FEB-05 1YS9 TITLE CRYSTAL STRUCTURE OF PHOSPHATASE SPY1043 FROM STREPTOCOCCUS PYOGENES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SPY1043; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 160490; SOURCE 4 STRAIN: M1 GAS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS, NYSGXRC TARGET T2098, UNKNOWN FUNCTION, PSI, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, NYSGRC EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,S.C.ALMO,S.K.BURLEY,NEW YORK SGX RESEARCH AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 6 20-OCT-21 1YS9 1 SEQADV REVDAT 5 03-FEB-21 1YS9 1 AUTHOR REVDAT 4 14-DEC-16 1YS9 1 TITLE REVDAT 3 13-JUL-11 1YS9 1 VERSN REVDAT 2 24-FEB-09 1YS9 1 VERSN REVDAT 1 15-FEB-05 1YS9 0 JRNL AUTH A.A.FEDOROV,E.V.FEDOROV,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN SPY1043 FROM JRNL TITL 2 STREPTOCOCCUS PYOGENES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.100 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 236536.950 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 13446 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 SET) : 0.226 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 682 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1239 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 56 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1942 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.17000 REMARK 3 B22 (A**2) : 12.58000 REMARK 3 B33 (A**2) : -7.41000 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.470 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.420 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.700 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.290 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 33.42 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YS9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-04; 23-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X9A; X9A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979; 0.97934, 0.97911, 0.97166 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL; DOUBLE CRYSTAL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13446 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM CITRATE, BISTRIS, PH 6.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 59.95950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.06800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.95950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.06800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.95950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.06800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.95950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.06800 REMARK 290 SMTRY3 8 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 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 VAL A 1 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 10 -74.20 -92.17 REMARK 500 GLU A 94 -167.86 -111.60 REMARK 500 THR A 210 -60.93 -101.55 REMARK 500 THR A 226 21.31 -67.02 REMARK 500 PHE A 229 -95.00 -34.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T2098 RELATED DB: TARGETDB DBREF 1YS9 A 1 254 UNP Q99ZW4 Q99ZW4_STRP1 1 254 SEQADV 1YS9 VAL A 1 UNP Q99ZW4 MET 1 ENGINEERED MUTATION SEQRES 1 A 254 VAL PRO TYR LYS GLY TYR LEU ILE ASP LEU ASP GLY THR SEQRES 2 A 254 ILE TYR GLN GLY LYS ASN ARG ILE PRO ALA GLY GLU ARG SEQRES 3 A 254 PHE ILE LYS ARG LEU GLN GLU ARG GLY ILE PRO TYR LEU SEQRES 4 A 254 LEU VAL THR ASN ASN THR THR ARG THR PRO GLU MET VAL SEQRES 5 A 254 GLN SER MET LEU ALA ASN GLN PHE HIS VAL GLU THR SER SEQRES 6 A 254 ILE GLU THR ILE TYR THR ALA THR MET ALA THR VAL ASP SEQRES 7 A 254 TYR MET ASN ASP MET ASN ARG GLY LYS THR ALA TYR VAL SEQRES 8 A 254 ILE GLY GLU THR GLY LEU LYS SER ALA ILE ALA ALA ALA SEQRES 9 A 254 GLY TYR VAL GLU GLU LEU GLU ASN PRO ALA TYR VAL VAL SEQRES 10 A 254 VAL GLY LEU ASP SER GLN VAL THR TYR GLU MET LEU ALA SEQRES 11 A 254 ILE ALA THR LEU ALA ILE GLN LYS GLY ALA LEU PHE ILE SEQRES 12 A 254 GLY THR ASN PRO ASP LEU ASN ILE PRO THR GLU ARG GLY SEQRES 13 A 254 LEU MET PRO GLY ALA GLY ALA LEU ASN ALA LEU LEU GLU SEQRES 14 A 254 ALA ALA THR ARG VAL LYS PRO VAL PHE ILE GLY LYS PRO SEQRES 15 A 254 ASN ALA ILE ILE MET ASN LYS SER LEU GLU VAL LEU GLY SEQRES 16 A 254 ILE GLN ARG SER GLU ALA VAL MET VAL GLY ASP ASN TYR SEQRES 17 A 254 LEU THR ASP ILE MET ALA GLY ILE GLN ASN ASP ILE ALA SEQRES 18 A 254 THR ILE LEU VAL THR THR GLY PHE THR ARG PRO GLU GLU SEQRES 19 A 254 VAL PRO THR LEU PRO ILE GLN PRO ASP HIS VAL LEU SER SEQRES 20 A 254 SER LEU ASP GLU TRP ARG LEU HELIX 1 1 ILE A 21 ARG A 34 1 14 HELIX 2 2 THR A 48 PHE A 60 1 13 HELIX 3 3 SER A 65 GLU A 67 5 3 HELIX 4 4 ALA A 72 ASN A 84 1 13 HELIX 5 5 GLU A 94 ALA A 104 1 11 HELIX 6 6 THR A 125 LYS A 138 1 14 HELIX 7 7 GLY A 160 ARG A 173 1 14 HELIX 8 8 ASN A 183 GLY A 195 1 13 HELIX 9 9 GLN A 197 SER A 199 5 3 HELIX 10 10 THR A 210 GLN A 217 1 8 HELIX 11 11 ARG A 231 LEU A 238 5 8 HELIX 12 12 SER A 248 TRP A 252 5 5 SHEET 1 A 6 ILE A 69 THR A 71 0 SHEET 2 A 6 TYR A 38 THR A 42 1 N LEU A 40 O TYR A 70 SHEET 3 A 6 GLY A 5 ILE A 8 1 N ILE A 8 O LEU A 39 SHEET 4 A 6 ALA A 201 GLY A 205 1 O VAL A 204 N LEU A 7 SHEET 5 A 6 ALA A 221 VAL A 225 1 O ALA A 221 N MET A 203 SHEET 6 A 6 HIS A 244 LEU A 246 1 O LEU A 246 N LEU A 224 SHEET 1 B 2 TYR A 15 GLN A 16 0 SHEET 2 B 2 ASN A 19 ARG A 20 -1 O ASN A 19 N GLN A 16 SHEET 1 C 5 VAL A 107 GLU A 108 0 SHEET 2 C 5 THR A 88 ILE A 92 1 N ALA A 89 O VAL A 107 SHEET 3 C 5 TYR A 115 VAL A 118 1 O VAL A 117 N ILE A 92 SHEET 4 C 5 LEU A 141 GLY A 144 1 O ILE A 143 N VAL A 118 SHEET 5 C 5 VAL A 177 PHE A 178 1 O VAL A 177 N PHE A 142 SHEET 1 D 2 ASN A 150 PRO A 152 0 SHEET 2 D 2 LEU A 157 PRO A 159 -1 O MET A 158 N ILE A 151 CISPEP 1 LYS A 181 PRO A 182 0 0.34 CRYST1 119.919 120.136 58.319 90.00 90.00 90.00 C 2 2 2 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 0.008339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017147 0.00000 MASTER 263 0 0 12 15 0 0 6 0 0 0 20 END