HEADER TRANSCRIPTION 23-APR-12 4ESF TITLE CRYSTAL STRUCTURE OF PADR-LIKE TRANSCRIPTIONAL REGULATOR (BCE3449) TITLE 2 FROM BACILLUS CEREUS STRAIN ATCC 10987 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PADR-LIKE TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 222523; SOURCE 4 STRAIN: ATCC 10987; SOURCE 5 GENE: BCE_3449; 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 3 13-SEP-23 4ESF 1 SEQADV REVDAT 2 12-DEC-12 4ESF 1 JRNL REVDAT 1 05-DEC-12 4ESF 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 6431 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.810 REMARK 3 FREE R VALUE TEST SET COUNT : 631 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 41.2753 - 3.7619 1.00 1274 123 0.2095 0.2452 REMARK 3 2 3.7619 - 2.9862 1.00 1163 134 0.2096 0.2762 REMARK 3 3 2.9862 - 2.6088 1.00 1141 127 0.2370 0.3065 REMARK 3 4 2.6088 - 2.3703 0.99 1129 130 0.2404 0.3418 REMARK 3 5 2.3703 - 2.2000 0.98 1093 117 0.2531 0.3929 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 : 42.42 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.070 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) : 7.78430 REMARK 3 B22 (A**2) : 7.78430 REMARK 3 B33 (A**2) : -15.56860 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 : 0.010 838 REMARK 3 ANGLE : 1.010 1123 REMARK 3 CHIRALITY : 0.057 127 REMARK 3 PLANARITY : 0.004 137 REMARK 3 DIHEDRAL : 15.088 322 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 3:77) REMARK 3 ORIGIN FOR THE GROUP (A): -1.1006 19.0679 -9.0211 REMARK 3 T TENSOR REMARK 3 T11: 0.3919 T22: 0.3799 REMARK 3 T33: 0.3297 T12: -0.0755 REMARK 3 T13: -0.0511 T23: 0.0939 REMARK 3 L TENSOR REMARK 3 L11: 9.8414 L22: 4.2877 REMARK 3 L33: 9.1348 L12: -1.4427 REMARK 3 L13: -1.1599 L23: 1.7684 REMARK 3 S TENSOR REMARK 3 S11: 0.2651 S12: 0.5337 S13: -0.4169 REMARK 3 S21: -0.1850 S22: -0.1418 S23: 0.5180 REMARK 3 S31: -0.0452 S32: -0.8739 S33: -0.1333 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 78:107) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7319 19.9321 4.6297 REMARK 3 T TENSOR REMARK 3 T11: 0.5214 T22: 0.2964 REMARK 3 T33: 0.3300 T12: -0.0743 REMARK 3 T13: -0.0048 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 1.5964 L22: 2.4167 REMARK 3 L33: 2.5483 L12: 0.5844 REMARK 3 L13: 2.0688 L23: -1.6199 REMARK 3 S TENSOR REMARK 3 S11: 0.3312 S12: -0.7374 S13: 0.5910 REMARK 3 S21: 0.1005 S22: -0.0389 S23: -0.5913 REMARK 3 S31: -0.0797 S32: -0.1427 S33: -0.2818 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 4ESF 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_1000072011. 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 : 8.0 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 : 6500 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 43.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.51100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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 (%): 41.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE, 9% (W/V) PEG 8000, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 60.03700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.97250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.97250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 90.05550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.97250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.97250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.01850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.97250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.97250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 90.05550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.97250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.97250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.01850 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 60.03700 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: 3060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 GLU A 2 REMARK 465 SER A 67 REMARK 465 ASP A 68 REMARK 465 MET A 69 REMARK 465 GLY A 70 REMARK 465 PRO A 71 REMARK 465 SER A 108 REMARK 465 ARG A 109 REMARK 465 TRP A 110 REMARK 465 SER A 111 REMARK 465 HIS A 112 REMARK 465 PRO A 113 REMARK 465 GLN A 114 REMARK 465 PHE A 115 REMARK 465 GLU A 116 REMARK 465 LYS A 117 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 OE1 GLU A 13 NH1 ARG A 53 1.98 REMARK 500 O HOH A 207 O HOH A 210 2.00 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 23 158.92 175.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ESB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PADR-LIKE TRANSCRIPTIONAL REGULATOR (BC4206) REMARK 900 FROM BACILLUS CEREUS STRAIN ATCC 14579 DBREF 4ESF A 1 105 UNP Q734F6 Q734F6_BACC1 1 105 SEQADV 4ESF SER A 106 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF ASN A 107 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF SER A 108 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF ARG A 109 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF TRP A 110 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF SER A 111 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF HIS A 112 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF PRO A 113 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF GLN A 114 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF PHE A 115 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF GLU A 116 UNP Q734F6 EXPRESSION TAG SEQADV 4ESF LYS A 117 UNP Q734F6 EXPRESSION TAG SEQRES 1 A 117 MET GLU ASN LEU THR GLU MET LEU LYS GLY SER LEU GLU SEQRES 2 A 117 GLY CYS VAL LEU GLU ILE ILE SER ARG ARG GLU THR TYR SEQRES 3 A 117 GLY TYR GLU ILE THR ARG HIS LEU ASN ASP LEU GLY PHE SEQRES 4 A 117 THR GLU VAL VAL GLU GLY THR VAL TYR THR ILE LEU VAL SEQRES 5 A 117 ARG LEU GLU LYS LYS LYS LEU VAL ASN ILE GLU LYS LYS SEQRES 6 A 117 PRO SER ASP MET GLY PRO PRO ARG LYS PHE TYR SER LEU SEQRES 7 A 117 ASN GLU ALA GLY ARG GLN GLU LEU GLU LEU PHE TRP LYS SEQRES 8 A 117 LYS TRP ASP PHE VAL SER SER LYS ILE ASN VAL LEU LYS SEQRES 9 A 117 SER SER ASN SER ARG TRP SER HIS PRO GLN PHE GLU LYS FORMUL 2 HOH *10(H2 O) HELIX 1 1 LEU A 4 ARG A 23 1 20 HELIX 2 2 TYR A 26 GLY A 38 1 13 HELIX 3 3 VAL A 43 LYS A 57 1 15 HELIX 4 4 ASN A 79 SER A 105 1 27 SHEET 1 A 2 VAL A 60 LYS A 65 0 SHEET 2 A 2 ARG A 73 LEU A 78 -1 O PHE A 75 N GLU A 63 CRYST1 43.945 43.945 120.074 90.00 90.00 90.00 P 43 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 0.022756 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008328 0.00000