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 6 14-FEB-24 1LJ9 1 REMARK 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