HEADER DNA BINDING PROTEIN 24-SEP-15 5DYM TITLE CRYSTAL STRUCTURE OF A PADR FAMILY TRANSCRIPTION REGULATOR FROM TITLE 2 HYPERVIRULENT CLOSTRIDIUM DIFFICILE R20291 - CDPADR_0991 TO 1.89 TITLE 3 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PADR-FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEPTOCLOSTRIDIUM DIFFICILE (STRAIN R20291); SOURCE 3 ORGANISM_TAXID: 645463; SOURCE 4 STRAIN: R20291; SOURCE 5 GENE: CDR20291_0991; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE80 KEYWDS PADR, WHTH DNA BINDING DOMAIN, HELIX TURN HELIX MOTIFS, TRANSCRIPTION KEYWDS 2 REGULATOR, PADR-S2, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.E.ISOM,E.A.KARR,S.K.MENON,A.H.WEST,G.B.RICHTER-ADDO REVDAT 3 27-SEP-23 5DYM 1 REMARK ATOM REVDAT 2 19-OCT-16 5DYM 1 JRNL REVDAT 1 05-OCT-16 5DYM 0 JRNL AUTH C.E.ISOM,S.K.MENON,L.M.THOMAS,A.H.WEST,G.B.RICHTER-ADDO, JRNL AUTH 2 E.A.KARR JRNL TITL CRYSTAL STRUCTURE AND DNA BINDING ACTIVITY OF A PADR FAMILY JRNL TITL 2 TRANSCRIPTION REGULATOR FROM HYPERVIRULENT CLOSTRIDIUM JRNL TITL 3 DIFFICILE R20291. JRNL REF BMC MICROBIOL. V. 16 231 2016 JRNL REFN ESSN 1471-2180 JRNL PMID 27716049 JRNL DOI 10.1186/S12866-016-0850-0 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 14293 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.240 REMARK 3 FREE R VALUE TEST SET COUNT : 749 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 34.3743 - 3.2387 0.99 2866 148 0.1974 0.2201 REMARK 3 2 3.2387 - 2.5709 1.00 2706 161 0.2333 0.2729 REMARK 3 3 2.5709 - 2.2460 1.00 2680 159 0.2234 0.2570 REMARK 3 4 2.2460 - 2.0407 0.99 2687 136 0.2173 0.2568 REMARK 3 5 2.0407 - 1.8944 0.97 2605 145 0.2455 0.2879 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.170 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.008 835 REMARK 3 ANGLE : 0.931 1111 REMARK 3 CHIRALITY : 0.044 113 REMARK 3 PLANARITY : 0.004 139 REMARK 3 DIHEDRAL : 14.741 335 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 5DYM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214037. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14302 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.894 REMARK 200 RESOLUTION RANGE LOW (A) : 34.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.01800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38210 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1XMA REMARK 200 REMARK 200 REMARK: SQUARE/BIPYRAMIDAL, CLEAR REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.1 M NACL, 100 MM HEPES (PH 7.5), REMARK 280 VAPOR DIFFUSION, HANGING DROP, 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 20.20400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 46.21000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.10200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.21000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 46.21000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.30600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.21000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.21000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 10.10200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 46.21000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.21000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.30600 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 20.20400 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: 2420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 40.40800 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 236 LIES ON A SPECIAL POSITION. 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 TRP A -7 REMARK 465 SER A -6 REMARK 465 HIS A -5 REMARK 465 PRO A -4 REMARK 465 GLN A -3 REMARK 465 PHE A -2 REMARK 465 GLU A -1 REMARK 465 LYS A 0 REMARK 465 MET A 1 REMARK 465 GLN A 2 REMARK 465 LEU A 3 REMARK 465 ASN A 4 REMARK 465 LYS A 5 REMARK 465 GLU A 6 REMARK 465 VAL A 7 REMARK 465 LEU A 8 REMARK 465 LYS A 9 REMARK 465 GLU A 41 REMARK 465 GLU A 107 REMARK 465 VAL A 108 REMARK 465 ASP A 109 DBREF 5DYM A 1 109 UNP C9YK90 C9YK90_PEPDR 1 109 SEQADV 5DYM TRP A -7 UNP C9YK90 EXPRESSION TAG SEQADV 5DYM SER A -6 UNP C9YK90 EXPRESSION TAG SEQADV 5DYM HIS A -5 UNP C9YK90 EXPRESSION TAG SEQADV 5DYM PRO A -4 UNP C9YK90 EXPRESSION TAG SEQADV 5DYM GLN A -3 UNP C9YK90 EXPRESSION TAG SEQADV 5DYM PHE A -2 UNP C9YK90 EXPRESSION TAG SEQADV 5DYM GLU A -1 UNP C9YK90 EXPRESSION TAG SEQADV 5DYM LYS A 0 UNP C9YK90 EXPRESSION TAG SEQRES 1 A 117 TRP SER HIS PRO GLN PHE GLU LYS MET GLN LEU ASN LYS SEQRES 2 A 117 GLU VAL LEU LYS GLY TYR ILE ASP ILE LEU ILE VAL SER SEQRES 3 A 117 ILE LEU GLU LYS LYS ASP CYS TYR GLY TYR GLU ILE ALA SEQRES 4 A 117 LYS GLN VAL ARG GLU ARG SER GLU PHE GLU LEU LYS GLU SEQRES 5 A 117 GLY THR MET TYR LEU ALA LEU LYS ARG MET GLU SER LYS SEQRES 6 A 117 ASN LEU ILE LYS SER TYR TYR SER ASN GLU GLN SER SER SEQRES 7 A 117 GLY GLY ARG ARG LYS TYR TYR ASN LEU THR ASN GLU GLY SEQRES 8 A 117 LYS ASP PHE LEU GLU ILE LYS LYS GLN GLU TRP ARG PHE SEQRES 9 A 117 ILE LYS LYS VAL MET ASN GLN PHE LEU GLY GLU VAL ASP FORMUL 2 HOH *36(H2 O) HELIX 1 AA1 TYR A 11 GLU A 21 1 11 HELIX 2 AA2 GLY A 27 SER A 38 1 12 HELIX 3 AA3 LYS A 43 LYS A 57 1 15 HELIX 4 AA4 THR A 80 GLY A 106 1 27 SHEET 1 AA1 3 CYS A 25 TYR A 26 0 SHEET 2 AA1 3 LYS A 75 LEU A 79 -1 O TYR A 77 N CYS A 25 SHEET 3 AA1 3 ILE A 60 TYR A 64 -1 N TYR A 63 O TYR A 76 CRYST1 92.420 92.420 40.408 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 0.010820 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024748 0.00000