HEADER TRANSCRIPTION 23-APR-12 4ESB TITLE CRYSTAL STRUCTURE OF PADR-LIKE TRANSCRIPTIONAL REGULATOR (BC4206) FROM TITLE 2 BACILLUS CEREUS STRAIN ATCC 14579 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, PADR FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 226900; SOURCE 4 STRAIN: ATCC 14579 / DSM 31; SOURCE 5 GENE: BC_4206; SOURCE 6 EXPRESSION_SYSTEM: LACTOCOCCUS LACTIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 746361; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SUBSP. CREMORIS NZ9000; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNSC8048 KEYWDS PADR FAMILY, TRANSCRIPTIONAL REGULATOR, DNA BINDING PROTEIN, WINGED- KEYWDS 2 HTH FOLD, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.FIBRIANSAH,A.T.KOVACS,O.P.KUIPERS,A.M.W.H.THUNNISSEN REVDAT 4 13-SEP-23 4ESB 1 REMARK SEQADV REVDAT 3 26-DEC-12 4ESB 1 REMARK REVDAT 2 12-DEC-12 4ESB 1 JRNL REVDAT 1 05-DEC-12 4ESB 0 JRNL AUTH G.FIBRIANSAH,A.T.KOVACS,T.J.POOL,M.BOONSTRA,O.P.KUIPERS, JRNL AUTH 2 A.M.THUNNISSEN JRNL TITL CRYSTAL STRUCTURES OF TWO TRANSCRIPTIONAL REGULATORS FROM JRNL TITL 2 BACILLUS CEREUS DEFINE THE CONSERVED STRUCTURAL FEATURES OF JRNL TITL 3 A PADR SUBFAMILY. JRNL REF PLOS ONE V. 7 48015 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 23189126 JRNL DOI 10.1371/JOURNAL.PONE.0048015 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8418 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.5016 - 3.6052 1.00 2792 127 0.1914 0.2036 REMARK 3 2 3.6052 - 2.8619 1.00 2649 121 0.1971 0.2471 REMARK 3 3 2.8619 - 2.5000 1.00 2585 144 0.2525 0.2727 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 44.13 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.37550 REMARK 3 B22 (A**2) : 11.37550 REMARK 3 B33 (A**2) : -22.75100 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 863 REMARK 3 ANGLE : 0.702 1152 REMARK 3 CHIRALITY : 0.039 125 REMARK 3 PLANARITY : 0.003 140 REMARK 3 DIHEDRAL : 15.622 328 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ESB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000072007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : DIAMOND (111)AND GE (220) REMARK 200 CRYSTALS REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8474 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 44.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.61100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 3HHH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17 M AMMONIUM SULFATE, 25.5% PEG REMARK 280 4000, 15% GLYCEROL, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 42.04150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.76800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.76800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.02075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.76800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.76800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.06225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.76800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.76800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.02075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.76800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.76800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.06225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.04150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 HIS A 2 REMARK 465 SER A 106 REMARK 465 ARG A 107 REMARK 465 TRP A 108 REMARK 465 SER A 109 REMARK 465 HIS A 110 REMARK 465 PRO A 111 REMARK 465 GLN A 112 REMARK 465 PHE A 113 REMARK 465 GLU A 114 REMARK 465 LYS A 115 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 22 O HOH A 309 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ESF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PADR-LIKE TRANSCRIPTIONAL REGULATOR (BCE3449) REMARK 900 FROM BACILLUS CEREUS STRAIN ATCC 10987 DBREF 4ESB A 1 105 UNP Q818P3 Q818P3_BACCR 1 105 SEQADV 4ESB SER A 106 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB ARG A 107 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB TRP A 108 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB SER A 109 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB HIS A 110 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB PRO A 111 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB GLN A 112 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB PHE A 113 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB GLU A 114 UNP Q818P3 EXPRESSION TAG SEQADV 4ESB LYS A 115 UNP Q818P3 EXPRESSION TAG SEQRES 1 A 115 MET HIS SER GLN MET LEU LYS GLY VAL LEU GLU GLY CYS SEQRES 2 A 115 ILE LEU TYR ILE ILE SER GLN GLU GLU VAL TYR GLY TYR SEQRES 3 A 115 GLU LEU SER THR LYS LEU ASN LYS HIS GLY PHE THR PHE SEQRES 4 A 115 VAL SER GLU GLY SER ILE TYR PRO LEU LEU LEU ARG MET SEQRES 5 A 115 GLN LYS GLU LYS LEU ILE GLU GLY THR LEU LYS ALA SER SEQRES 6 A 115 SER LEU GLY PRO LYS ARG LYS TYR TYR HIS ILE THR ASP SEQRES 7 A 115 LYS GLY LEU GLU GLN LEU GLU GLU PHE LYS GLN SER TRP SEQRES 8 A 115 GLY MET VAL SER THR THR VAL ASN ASN LEU LEU GLN GLY SEQRES 9 A 115 GLU SER ARG TRP SER HIS PRO GLN PHE GLU LYS HET SO4 A 201 5 HET GOL A 202 6 HET GOL A 203 6 HET GOL A 204 6 HET GOL A 205 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 O4 S 2- FORMUL 3 GOL 4(C3 H8 O3) FORMUL 7 HOH *17(H2 O) HELIX 1 1 VAL A 9 GLU A 21 1 13 HELIX 2 2 GLY A 25 HIS A 35 1 11 HELIX 3 3 SER A 41 GLU A 55 1 15 HELIX 4 4 THR A 77 LEU A 102 1 26 SHEET 1 A 3 VAL A 23 TYR A 24 0 SHEET 2 A 3 LYS A 70 ILE A 76 -1 O TYR A 74 N VAL A 23 SHEET 3 A 3 ILE A 58 ALA A 64 -1 N GLU A 59 O HIS A 75 SITE 1 AC1 6 ARG A 71 LYS A 72 ASP A 78 HOH A 301 SITE 2 AC1 6 HOH A 305 HOH A 311 SITE 1 AC2 3 GLU A 22 LYS A 63 ALA A 64 SITE 1 AC3 2 LYS A 31 HIS A 35 SITE 1 AC4 8 ILE A 18 SER A 19 GLU A 21 GLU A 22 SITE 2 AC4 8 SER A 29 GLU A 42 HIS A 75 ILE A 76 SITE 1 AC5 5 TYR A 24 SER A 65 SER A 66 ARG A 71 SITE 2 AC5 5 TYR A 73 CRYST1 73.536 73.536 84.083 90.00 90.00 90.00 P 41 21 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 0.013599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011893 0.00000