HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 30-DEC-08 3FOJ TITLE CRYSTAL STRUCTURE OF SSP1007 FROM STAPHYLOCOCCUS SAPROPHYTICUS SUBSP. TITLE 2 SAPROPHYTICUS. NORTHEAST STRUCTURAL 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 STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, UNKNOWN KEYWDS 3 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 2 27-NOV-24 3FOJ 1 REMARK LINK REVDAT 1 20-JAN-09 3FOJ 0 JRNL AUTH J.SEETHARAMAN,M.ABASHIDZE,H.WANG,H.JANJUA,E.L.FOOTE,R.XIAO, JRNL AUTH 2 J.K.EVERETT,T.B.ACTON,B.ROST,G.T.MONTELIONE,J.F.HUNT,L.TONG JRNL TITL CRYSTAL STRUCTURE OF SSP1007 FROM STAPHYLOCOCCUS JRNL TITL 2 SAPROPHYTICUS SUBSP. SAPROPHYTICUS. NORTHEAST STRUCTURAL JRNL TITL 3 GENOMICS TARGET SYR101A. JRNL REF TO BE PUBLISHED JRNL REFN 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) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000050845. 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 : CCD 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 : 16.00 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 (%): 27.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150MM MGSO4, 100 MM NA3 CITRATE, 20% REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 5 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