HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 30-DEC-08 3FOJ TITLE CRYSTAL STRUCTURE OF SSP1007 FROM STAPHYLOCOCCUS TITLE 2 SAPROPHYTICUS SUBSP. SAPROPHYTICUS. NORTHEAST STRUCTURAL TITLE 3 GENOMICS TARGET SYR101A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS SAPROPHYTICUS SUBSP. SOURCE 3 SAPROPHYTICUS ATCC 15305; SOURCE 4 ORGANISM_TAXID: 342451; SOURCE 5 GENE: SSP1007; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN SSP1007, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.SEETHARAMAN,M.ABASHIDZE,H.WANG,H.JANJUA,E.L.FOOTE,R.XIAO, AUTHOR 2 J.K.EVERETT,T.B.ACTON,B.ROST,G.T.MONTELIONE,J.F.HUNT,L.TONG, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 1 20-JAN-09 3FOJ 0 JRNL AUTH J.SEETHARAMAN,M.ABASHIDZE,H.WANG,H.JANJUA, JRNL AUTH 2 E.L.FOOTE,R.XIAO,J.K.EVERETT,T.B.ACTON,B.ROST, JRNL AUTH 3 G.T.MONTELIONE,J.F.HUNT,L.TONG JRNL TITL CRYSTAL STRUCTURE OF SSP1007 FROM STAPHYLOCOCCUS JRNL TITL 2 SAPROPHYTICUS SUBSP. SAPROPHYTICUS. NORTHEAST JRNL TITL 3 STRUCTURAL GENOMICS TARGET SYR101A. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 119624.420 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 18913 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) : 0.194 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 951 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 0.99 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 768 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.53000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -1.48000 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) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.07 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.02 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.75 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) : 1.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.720 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.570 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.550 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 42.80 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: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3FOJ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB050845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19428 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36000 REMARK 200 FOR SHELL : 16.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150MM MGSO4, 100 MM NA3 CITRATE, REMARK 280 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 15.34600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.42750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.06500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.42750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.34600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.06500 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 300 REMARK: MONOMER 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 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 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 40 O REMARK 620 2 THR A 40 OG1 69.1 REMARK 620 3 HOH A 143 O 74.8 134.5 REMARK 620 4 HOH A 146 O 97.6 77.3 80.9 REMARK 620 N 1 2 3 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 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SYR101A RELATED DB: TARGETDB DBREF 3FOJ A 1 97 UNP Q49YI7 Q49YI7_STAS1 1 97 SEQADV 3FOJ LEU A 98 UNP Q49YI7 EXPRESSION TAG SEQADV 3FOJ GLU A 99 UNP Q49YI7 EXPRESSION TAG SEQADV 3FOJ HIS A 100 UNP Q49YI7 EXPRESSION TAG SEQRES 1 A 100 MSE GLU SER ILE THR VAL THR GLU LEU LYS GLU LYS ILE SEQRES 2 A 100 LEU ASP ALA ASN PRO VAL ASN ILE VAL ASP VAL ARG THR SEQRES 3 A 100 ASP GLN GLU THR ALA MSE GLY ILE ILE PRO GLY ALA GLU SEQRES 4 A 100 THR ILE PRO MSE ASN SER ILE PRO ASP ASN LEU ASN TYR SEQRES 5 A 100 PHE ASN ASP ASN GLU THR TYR TYR ILE ILE CYS LYS ALA SEQRES 6 A 100 GLY GLY ARG SER ALA GLN VAL VAL GLN TYR LEU GLU GLN SEQRES 7 A 100 ASN GLY VAL ASN ALA VAL ASN VAL GLU GLY GLY MSE ASP SEQRES 8 A 100 GLU PHE GLY ASP GLU GLY LEU GLU HIS MODRES 3FOJ MSE A 1 MET SELENOMETHIONINE MODRES 3FOJ MSE A 32 MET SELENOMETHIONINE MODRES 3FOJ MSE A 43 MET SELENOMETHIONINE MODRES 3FOJ MSE A 90 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 32 8 HET MSE A 43 8 HET MSE A 90 8 HET NA A 101 1 HETNAM MSE SELENOMETHIONINE HETNAM NA SODIUM ION FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 NA NA 1+ FORMUL 3 HOH *123(H2 O) HELIX 1 1 THR A 5 LYS A 12 1 8 HELIX 2 2 ILE A 13 ASP A 15 5 3 HELIX 3 3 THR A 26 ALA A 31 1 6 HELIX 4 4 PRO A 42 PHE A 53 5 12 HELIX 5 5 GLY A 66 GLN A 78 1 13 HELIX 6 6 GLY A 88 GLY A 94 1 7 SHEET 1 A 5 SER A 3 ILE A 4 0 SHEET 2 A 5 ASN A 82 VAL A 86 1 O ASN A 85 N ILE A 4 SHEET 3 A 5 THR A 58 ILE A 62 1 N ILE A 61 O VAL A 84 SHEET 4 A 5 ASN A 20 ASP A 23 1 N ASN A 20 O TYR A 60 SHEET 5 A 5 GLU A 39 THR A 40 1 O GLU A 39 N ASP A 23 LINK C MSE A 1 N GLU A 2 1555 1555 1.33 LINK C ALA A 31 N MSE A 32 1555 1555 1.33 LINK C MSE A 32 N GLY A 33 1555 1555 1.33 LINK C PRO A 42 N MSE A 43 1555 1555 1.33 LINK C MSE A 43 N ASN A 44 1555 1555 1.33 LINK C GLY A 89 N MSE A 90 1555 1555 1.33 LINK C MSE A 90 N ASP A 91 1555 1555 1.33 LINK O THR A 40 NA NA A 101 1555 1555 2.46 LINK OG1 THR A 40 NA NA A 101 1555 1555 2.65 LINK NA NA A 101 O HOH A 143 1555 1555 2.69 LINK NA NA A 101 O HOH A 146 1555 1555 2.88 SITE 1 AC1 7 THR A 40 GLU A 96 HOH A 118 HOH A 126 SITE 2 AC1 7 HOH A 143 HOH A 146 HOH A 160 CRYST1 30.692 42.130 58.855 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 0.032582 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023736 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016991 0.00000 HETATM 1 N MSE A 1 7.053 12.335 9.414 1.00 20.86 N HETATM 2 CA MSE A 1 7.225 13.373 10.469 1.00 20.72 C HETATM 3 C MSE A 1 7.032 12.773 11.852 1.00 18.83 C HETATM 4 O MSE A 1 6.201 11.888 12.046 1.00 19.16 O HETATM 5 CB MSE A 1 6.215 14.507 10.268 1.00 23.98 C HETATM 6 CG MSE A 1 6.247 15.556 11.366 1.00 26.90 C HETATM 7 SE MSE A 1 4.896 16.909 11.146 1.00 33.76 SE HETATM 8 CE MSE A 1 3.408 15.971 11.938 1.00 31.43 C