HEADER DNA BINDING PROTEIN 21-JAN-24 8XZU TITLE HOSA TRANSCRIPTIONAL REGULATOR FROM ENTEROPATHOGENIC ESCHERICHIA COLI TITLE 2 O127:H6 (STRAIN E2348/69) BOUND WITH 4-HYDROXY BENZOIC ACID - TITLE 3 CONFORMATION II AT 2.33 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR HOSA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HOSA PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O127:H6 STR. E2348/69; SOURCE 3 ORGANISM_TAXID: 574521; SOURCE 4 GENE: HOSA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ANTIBIOTIC RESISTANCE, MARR TRANSCRIPTION FACTOR, HOSA, KEYWDS 2 ENTEROPATHOGENIC ESCHERICHIA COLI, DNA BINDING PROTEIN, PARABEN EXPDTA X-RAY DIFFRACTION AUTHOR K.MANJUNATH,A.GOSWAMI REVDAT 1 28-AUG-24 8XZU 0 JRNL AUTH A.GOSWAMI,S.ULLAH,J.A.BRITO JRNL TITL HORIZONTALLY ACQUIRED HOSA TRANSCRIPTION FACTOR BOUND WITH JRNL TITL 2 4-HYDROXY-BENZOIC ACID EXHIBITS UNIQUE TUG-OF-WATER JRNL TITL 3 DYNAMICS. JRNL REF BIORXIV 2024 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2024.04.24.590444 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9848 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 985 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 67.2900 - 4.4700 1.00 1371 153 0.2079 0.2014 REMARK 3 2 4.4600 - 3.5400 1.00 1278 141 0.2050 0.2256 REMARK 3 3 3.5400 - 3.0900 1.00 1270 142 0.2294 0.2855 REMARK 3 4 3.0900 - 2.8100 1.00 1246 138 0.2630 0.2939 REMARK 3 5 2.8100 - 2.6100 1.00 1247 139 0.2895 0.2837 REMARK 3 6 2.6100 - 2.4600 1.00 1229 136 0.2948 0.3387 REMARK 3 7 2.4600 - 2.3300 1.00 1222 136 0.3263 0.3658 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.41 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 : 0.001 1091 REMARK 3 ANGLE : 0.397 1468 REMARK 3 CHIRALITY : 0.032 162 REMARK 3 PLANARITY : 0.002 192 REMARK 3 DIHEDRAL : 4.716 150 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.7369 -11.2869 -7.3324 REMARK 3 T TENSOR REMARK 3 T11: 0.2643 T22: 0.2817 REMARK 3 T33: 0.2749 T12: -0.0156 REMARK 3 T13: 0.0159 T23: -0.0455 REMARK 3 L TENSOR REMARK 3 L11: 2.6012 L22: 2.3691 REMARK 3 L33: 4.9331 L12: -0.6104 REMARK 3 L13: 1.8746 L23: -1.3847 REMARK 3 S TENSOR REMARK 3 S11: -0.3073 S12: -0.1327 S13: 0.3776 REMARK 3 S21: 0.0797 S22: 0.0820 S23: 0.0058 REMARK 3 S31: -0.1218 S32: -0.5782 S33: 0.2207 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.0048 -2.9889 -9.2739 REMARK 3 T TENSOR REMARK 3 T11: 0.4405 T22: 1.3374 REMARK 3 T33: 0.6071 T12: 0.2148 REMARK 3 T13: -0.1917 T23: -0.2419 REMARK 3 L TENSOR REMARK 3 L11: 1.0774 L22: 2.0951 REMARK 3 L33: 0.5792 L12: -0.7206 REMARK 3 L13: -0.7868 L23: 0.4284 REMARK 3 S TENSOR REMARK 3 S11: -0.4796 S12: -1.3282 S13: 1.0522 REMARK 3 S21: 0.4265 S22: 0.5920 S23: -0.0999 REMARK 3 S31: -0.3099 S32: -0.7816 S33: -0.0327 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.5336 -24.2622 -10.5483 REMARK 3 T TENSOR REMARK 3 T11: 0.4775 T22: 0.2539 REMARK 3 T33: 0.3902 T12: -0.0267 REMARK 3 T13: 0.0324 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 1.2787 L22: 3.1683 REMARK 3 L33: 3.1878 L12: -1.0928 REMARK 3 L13: 1.3181 L23: -1.1844 REMARK 3 S TENSOR REMARK 3 S11: 0.2866 S12: 0.2254 S13: -0.3437 REMARK 3 S21: -0.6257 S22: -0.0969 S23: 0.1868 REMARK 3 S31: 0.9970 S32: 0.1691 S33: -0.2150 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TLS REFINEMENT AND PDB REDO WERE USED REMARK 3 IN INTERMEDIATE STEPS OF REFINEMENT. LAST REFINEMENT WAS FROM REMARK 3 PHENIX.REFINE ONLY. REMARK 4 REMARK 4 8XZU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.4.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.13 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9878 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 67.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 1.52400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: ROD SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM PHOSPHATE DIBASIC/ POTASSIUM REMARK 280 PHOSPHATE MONOBASIC, SODIUM CHLORIDE, PEG 200, PH 6.2, REMARK 280 MICROBATCH, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 47.63500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 71.45250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.81750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.63500 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 23.81750 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 71.45250 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: MONOMERIC 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 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 THR A 135 REMARK 465 LEU A 136 REMARK 465 GLU A 137 REMARK 465 HIS A 138 REMARK 465 HIS A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 53 CG CD OE1 OE2 REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 ARG A 130 CG CD NE CZ NH1 NH2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8XB7 RELATED DB: PDB REMARK 900 THIS STRUCTURE WAS SOLVED AT 2.6 ANGSTROM RESOLUTION. DBREF 8XZU A 1 135 UNP P69782 HOSA_ECO27 1 135 SEQADV 8XZU LEU A 136 UNP P69782 EXPRESSION TAG SEQADV 8XZU GLU A 137 UNP P69782 EXPRESSION TAG SEQADV 8XZU HIS A 138 UNP P69782 EXPRESSION TAG SEQADV 8XZU HIS A 139 UNP P69782 EXPRESSION TAG SEQADV 8XZU HIS A 140 UNP P69782 EXPRESSION TAG SEQADV 8XZU HIS A 141 UNP P69782 EXPRESSION TAG SEQADV 8XZU HIS A 142 UNP P69782 EXPRESSION TAG SEQADV 8XZU HIS A 143 UNP P69782 EXPRESSION TAG SEQRES 1 A 143 MET ALA LEU ARG ASN LYS ALA PHE HIS GLN LEU ARG GLN SEQRES 2 A 143 LEU PHE GLN GLN HIS THR ALA ARG TRP GLN HIS GLU LEU SEQRES 3 A 143 PRO ASP LEU THR LYS PRO GLN TYR ALA VAL MET ARG ALA SEQRES 4 A 143 ILE ALA ASP LYS PRO GLY ILE GLU GLN VAL ALA LEU ILE SEQRES 5 A 143 GLU ALA ALA VAL SER THR LYS ALA THR LEU ALA GLU MET SEQRES 6 A 143 LEU ALA ARG MET GLU ASN ARG GLY LEU VAL ARG ARG GLU SEQRES 7 A 143 HIS ASP ALA ALA ASP LYS ARG ARG ARG PHE VAL TRP LEU SEQRES 8 A 143 THR ALA GLU GLY GLU LYS VAL LEU ALA ALA ALA ILE PRO SEQRES 9 A 143 ILE GLY ASP SER VAL ASP GLU GLU PHE LEU GLY ARG LEU SEQRES 10 A 143 SER ALA GLU GLU GLN GLU LEU PHE MET GLN LEU VAL ARG SEQRES 11 A 143 LYS MET MET ASN THR LEU GLU HIS HIS HIS HIS HIS HIS HET PHB A 201 10 HET PEG A 202 7 HETNAM PHB P-HYDROXYBENZOIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 PHB C7 H6 O3 FORMUL 3 PEG C4 H10 O3 FORMUL 4 HOH *28(H2 O) HELIX 1 AA1 ALA A 2 ASN A 5 5 4 HELIX 2 AA2 LYS A 6 LEU A 26 1 21 HELIX 3 AA3 THR A 30 LYS A 43 1 14 HELIX 4 AA4 LEU A 51 VAL A 56 1 6 HELIX 5 AA5 THR A 58 ARG A 72 1 15 HELIX 6 AA6 THR A 92 GLY A 115 1 24 HELIX 7 AA7 SER A 118 MET A 132 1 15 SHEET 1 AA1 3 ILE A 46 GLU A 47 0 SHEET 2 AA1 3 ARG A 87 LEU A 91 -1 O VAL A 89 N ILE A 46 SHEET 3 AA1 3 VAL A 75 HIS A 79 -1 N ARG A 76 O TRP A 90 CRYST1 67.290 67.290 95.270 90.00 90.00 90.00 P 43 2 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 0.014861 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010496 0.00000