HEADER TRANSCRIPTION 19-APR-02 1LJ9 TITLE THE CRYSTAL STRUCTURE OF THE TRANSCRIPTIONAL REGULATOR SLYA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR SLYA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 GENE: REF02436; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEX1 KEYWDS HTH DNA BINDING PROTEIN, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, KEYWDS 3 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.Y.WU,R.G.ZHANG,P.GORNICKI,A.JOACHIMIAK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 5 11-OCT-17 1LJ9 1 REMARK REVDAT 4 24-FEB-09 1LJ9 1 VERSN REVDAT 3 25-JAN-05 1LJ9 1 JRNL REVDAT 2 18-JAN-05 1LJ9 1 AUTHOR KEYWDS REMARK REVDAT 1 21-JAN-03 1LJ9 0 JRNL AUTH R.Y.WU,R.G.ZHANG,O.ZAGNITKO,I.DEMENTIEVA,N.MALTZEV, JRNL AUTH 2 J.D.WATSON,R.LASKOWSKI,P.GORNICKI,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS SLYA-LIKE JRNL TITL 2 TRANSCRIPTIONAL FACTOR JRNL REF J.BIOL.CHEM. V. 278 20240 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12649270 JRNL DOI 10.1074/JBC.M300292200 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 38.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 472197.950 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.4 REMARK 3 NUMBER OF REFLECTIONS : 57399 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) : 0.248 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2819 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7310 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 371 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2330 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 289 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -2.95000 REMARK 3 B33 (A**2) : 3.08000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 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) : 0.590 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.910 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.320 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.820 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 45.04 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FRIEDEL'S PAIRS WERE INCLUDED IN REMARK 3 THE REFINEMENT. REMARK 4 REMARK 4 1LJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000015987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793, 0.9795, 0.95354 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32997 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 6.295 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.2600 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 (%) : 79.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.83 REMARK 200 R MERGE FOR SHELL (I) : 0.39800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, 22%, 0.1M HEPES, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING 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 21.75600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.99950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.21450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.99950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.75600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.21450 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: THE FUNCTIONAL DIMER CONSISTS OF REMARK 300 MOLA AND MOLB. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 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 LYS B 144 REMARK 465 GLY B 145 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 LYS A 55 45.24 72.34 REMARK 500 LYS A 144 23.24 -76.85 REMARK 500 LYS B 55 42.00 72.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC100 RELATED DB: TARGETDB DBREF 1LJ9 A 2 145 UNP Q82ZP8 Q82ZP8_ENTFA 2 145 DBREF 1LJ9 B 2 145 UNP Q82ZP8 Q82ZP8_ENTFA 2 145 SEQRES 1 A 144 THR ASP ILE LEU ARG GLU ILE GLY MET ILE ALA ARG ALA SEQRES 2 A 144 LEU ASP SER ILE SER ASN ILE GLU PHE LYS GLU LEU SER SEQRES 3 A 144 LEU THR ARG GLY GLN TYR LEU TYR LEU VAL ARG VAL CYS SEQRES 4 A 144 GLU ASN PRO GLY ILE ILE GLN GLU LYS ILE ALA GLU LEU SEQRES 5 A 144 ILE LYS VAL ASP ARG THR THR ALA ALA ARG ALA ILE LYS SEQRES 6 A 144 ARG LEU GLU GLU GLN GLY PHE ILE TYR ARG GLN GLU ASP SEQRES 7 A 144 ALA SER ASN LYS LYS ILE LYS ARG ILE TYR ALA THR GLU SEQRES 8 A 144 LYS GLY LYS ASN VAL TYR PRO ILE ILE VAL ARG GLU ASN SEQRES 9 A 144 GLN HIS SER ASN GLN VAL ALA LEU GLN GLY LEU SER GLU SEQRES 10 A 144 VAL GLU ILE SER GLN LEU ALA ASP TYR LEU VAL ARG MET SEQRES 11 A 144 ARG LYS ASN VAL SER GLU ASP TRP GLU PHE VAL LYS LYS SEQRES 12 A 144 GLY SEQRES 1 B 144 THR ASP ILE LEU ARG GLU ILE GLY MET ILE ALA ARG ALA SEQRES 2 B 144 LEU ASP SER ILE SER ASN ILE GLU PHE LYS GLU LEU SER SEQRES 3 B 144 LEU THR ARG GLY GLN TYR LEU TYR LEU VAL ARG VAL CYS SEQRES 4 B 144 GLU ASN PRO GLY ILE ILE GLN GLU LYS ILE ALA GLU LEU SEQRES 5 B 144 ILE LYS VAL ASP ARG THR THR ALA ALA ARG ALA ILE LYS SEQRES 6 B 144 ARG LEU GLU GLU GLN GLY PHE ILE TYR ARG GLN GLU ASP SEQRES 7 B 144 ALA SER ASN LYS LYS ILE LYS ARG ILE TYR ALA THR GLU SEQRES 8 B 144 LYS GLY LYS ASN VAL TYR PRO ILE ILE VAL ARG GLU ASN SEQRES 9 B 144 GLN HIS SER ASN GLN VAL ALA LEU GLN GLY LEU SER GLU SEQRES 10 B 144 VAL GLU ILE SER GLN LEU ALA ASP TYR LEU VAL ARG MET SEQRES 11 B 144 ARG LYS ASN VAL SER GLU ASP TRP GLU PHE VAL LYS LYS SEQRES 12 B 144 GLY FORMUL 3 HOH *289(H2 O) HELIX 1 1 ASP A 3 PHE A 23 1 21 HELIX 2 2 LYS A 24 SER A 27 5 4 HELIX 3 3 GLY A 31 ASN A 42 1 12 HELIX 4 4 GLN A 47 LYS A 55 1 9 HELIX 5 5 ASP A 57 GLN A 71 1 15 HELIX 6 6 THR A 91 LEU A 113 1 23 HELIX 7 7 SER A 117 LYS A 144 1 28 HELIX 8 8 ASP B 3 PHE B 23 1 21 HELIX 9 9 LYS B 24 SER B 27 5 4 HELIX 10 10 GLY B 31 ASN B 42 1 12 HELIX 11 11 GLN B 47 LYS B 55 1 9 HELIX 12 12 ASP B 57 GLN B 71 1 15 HELIX 13 13 THR B 91 LEU B 113 1 23 HELIX 14 14 SER B 117 LYS B 143 1 27 SHEET 1 A 3 ILE A 45 ILE A 46 0 SHEET 2 A 3 LYS A 86 ALA A 90 -1 O ILE A 88 N ILE A 45 SHEET 3 A 3 ILE A 74 GLU A 78 -1 N TYR A 75 O TYR A 89 SHEET 1 B 3 ILE B 45 ILE B 46 0 SHEET 2 B 3 LYS B 86 ALA B 90 -1 O ILE B 88 N ILE B 45 SHEET 3 B 3 ILE B 74 GLU B 78 -1 N GLN B 77 O ARG B 87 CRYST1 43.512 48.429 125.999 90.00 90.00 90.00 P 21 21 21 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 0.022982 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020649 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007937 0.00000 MASTER 252 0 0 14 6 0 0 6 0 0 0 24 END