HEADER DNA BINDING PROTEIN 02-MAR-25 9QBC TITLE CRYSTAL STRUCTURE OF BRACHYSPIRA HAMPSONII PADR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PADR-FAMILY TRANSCRIPTIONAL REGULATOR PADR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: C-TERMINAL STREP-TAG, GENBANK WP_107926394.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRACHYSPIRA HAMPSONII; SOURCE 3 ORGANISM_TAXID: 1287055; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTIONAL REGULATOR, PADR FAMILY, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.W.H.THUNNISSEN,H.J.ROZEBOOM,B.BROUWER,G.ROELFES REVDAT 1 11-MAR-26 9QBC 0 JRNL AUTH B.BROUWER,H.J.ROZEBOOM,A.M.W.H.THUNNISSEN,G.ROELFES JRNL TITL EXPLORING UNCHARACTERIZED PADR PROTEINS FOR ARTIFICIAL JRNL TITL 2 ENZYME DESIGN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.2_5419: ???) 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8540 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 408 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 26.9300 - 2.9600 1.00 2825 154 0.2035 0.2668 REMARK 3 2 2.9500 - 2.3500 1.00 2664 132 0.2801 0.3096 REMARK 3 3 2.3500 - 2.0500 1.00 2643 122 0.2645 0.2840 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.770 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 : 0.011 887 REMARK 3 ANGLE : 1.190 1188 REMARK 3 CHIRALITY : 0.057 126 REMARK 3 PLANARITY : 0.017 150 REMARK 3 DIHEDRAL : 5.733 117 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -12.3397 9.4522 2.5685 REMARK 3 T TENSOR REMARK 3 T11: 0.3423 T22: 0.2519 REMARK 3 T33: 0.3233 T12: 0.0151 REMARK 3 T13: -0.0635 T23: 0.0242 REMARK 3 L TENSOR REMARK 3 L11: 2.5279 L22: 5.2976 REMARK 3 L33: 2.0364 L12: -2.4294 REMARK 3 L13: -1.2031 L23: 1.8615 REMARK 3 S TENSOR REMARK 3 S11: 0.2374 S12: 0.2291 S13: 0.2153 REMARK 3 S21: -0.5016 S22: -0.3367 S23: -0.0019 REMARK 3 S31: -0.3688 S32: 0.0280 S33: 0.1266 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 9QBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292145881. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : HELIOS MX MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8597 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 1.07200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH REMARK 280 8.5, 1.26 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K 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 53.86300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.13300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.13300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.93150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.13300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.13300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 80.79450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.13300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.13300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.93150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.13300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.13300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 80.79450 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 53.86300 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: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 ASN A 2 REMARK 465 ILE A 3 REMARK 465 GLU A 109 REMARK 465 GLY A 110 REMARK 465 GLY A 111 REMARK 465 SER A 112 REMARK 465 GLY A 113 REMARK 465 GLY A 114 REMARK 465 SER A 115 REMARK 465 ALA A 116 REMARK 465 TRP A 117 REMARK 465 SER A 118 REMARK 465 HIS A 119 REMARK 465 PRO A 120 REMARK 465 GLN A 121 REMARK 465 PHE A 122 REMARK 465 GLU A 123 REMARK 465 LYS A 124 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 75 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9QBC A 1 124 PDB 9QBC 9QBC 1 124 SEQRES 1 A 124 MET ASN ILE GLU SER ASP ILE ILE ARG GLY HIS ILE ASP SEQRES 2 A 124 ALA VAL VAL LEU ASN PHE LEU LYS ASP ASN ASP SER TYR SEQRES 3 A 124 GLY TYR GLU LEU SER LYS LEU ILE THR ASP LYS THR ASN SEQRES 4 A 124 GLY GLU TYR GLU ILE ASN GLY GLN THR LEU TYR SER ALA SEQRES 5 A 124 ILE ASP ARG LEU GLU SER LYS LYS LEU ILE GLU GLY TYR SEQRES 6 A 124 TRP GLY ASP GLU SER GLN GLY GLY ARG ARG LYS TYR TYR SEQRES 7 A 124 ARG ILE THR GLU GLU GLY LYS LYS PHE LEU LYS GLU GLU SEQRES 8 A 124 ARG ASP ILE TRP LEU PHE THR LYS LYS ILE ILE ASP LYS SEQRES 9 A 124 LEU LEU ASP ILE GLU GLY GLY SER GLY GLY SER ALA TRP SEQRES 10 A 124 SER HIS PRO GLN PHE GLU LYS FORMUL 2 HOH *9(H2 O) HELIX 1 AA1 GLU A 4 GLY A 10 1 7 HELIX 2 AA2 HIS A 11 ASN A 23 1 13 HELIX 3 AA3 TYR A 26 THR A 38 1 13 HELIX 4 AA4 ASN A 45 LYS A 59 1 15 HELIX 5 AA5 THR A 81 LEU A 106 1 26 SHEET 1 AA1 2 ILE A 62 TRP A 66 0 SHEET 2 AA1 2 LYS A 76 ILE A 80 -1 O TYR A 77 N TYR A 65 CRYST1 48.266 48.266 107.726 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 0.020719 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009283 0.00000 MASTER 271 0 0 5 2 0 0 6 882 1 0 10 END