HEADER DNA BINDING PROTEIN 17-OCT-23 8WSV TITLE PRE-BINDING STRUCTURE OF HOSA TRANSCRIPTIONAL REGULATOR FROM TITLE 2 ENTEROPATHOGENIC ESCHERICHIA COLI O127:H6 (STRAIN E2348/69) IN TITLE 3 PRESENCE OF SUB OPTIMAL CONCENTRATION OF 4-HYDROXY BENZOIC ACID 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 EXPDTA X-RAY DIFFRACTION AUTHOR A.GOSWAMI,R.RAJU,M.KASARLA,S.ULLAH REVDAT 1 28-AUG-24 8WSV 0 JRNL AUTH G.ARPITA,R.RUKMINI,K.MALLESHAM,U.SAMEE JRNL TITL PRE-BINDING STRUCTURE OF HOSA TRANSCRIPTIONAL REGULATOR FROM JRNL TITL 2 ENTEROPATHOGENIC ESCHERICHIA COLI O127:H6 (STRAIN E2348/69) JRNL TITL 3 IN PRESENCE OF SUB OPTIMAL CONCENTRATION OF 4-HYDROXY JRNL TITL 4 BENZOIC ACID JRNL REF BIORXIV 2024 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2024.04.24.590444 REMARK 2 REMARK 2 RESOLUTION. 2.01 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 14925 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1495 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 42.6500 - 4.4600 0.99 1359 152 0.2092 0.2355 REMARK 3 2 4.4600 - 3.5400 0.98 1261 141 0.1971 0.2155 REMARK 3 3 3.5400 - 3.0900 0.98 1253 139 0.2317 0.2221 REMARK 3 4 3.0900 - 2.8100 0.98 1217 136 0.2537 0.2563 REMARK 3 5 2.8100 - 2.6100 0.98 1235 137 0.2555 0.2791 REMARK 3 6 2.6100 - 2.4600 0.98 1196 133 0.2528 0.2599 REMARK 3 7 2.4600 - 2.3300 0.97 1197 133 0.2313 0.2898 REMARK 3 8 2.3300 - 2.2300 0.96 1187 132 0.2391 0.2610 REMARK 3 9 2.2300 - 2.1500 0.96 1180 131 0.2409 0.2933 REMARK 3 10 2.1500 - 2.0700 0.97 1169 131 0.2432 0.2872 REMARK 3 11 2.0700 - 2.0100 0.96 1176 130 0.2421 0.2876 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) : 23.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.45 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 : 0.002 1075 REMARK 3 ANGLE : 0.432 1447 REMARK 3 CHIRALITY : 0.030 158 REMARK 3 PLANARITY : 0.003 190 REMARK 3 DIHEDRAL : 4.172 144 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: TLS REFINEMENT ALONG WITH OCCUPANCY WAS REMARK 3 CARRIED OUT FOR FEW STEPS. ONCE THE PARTIAL DENSITY OF THE REMARK 3 LIGAND WAS CLEAR WHICH ALIGNED PERFECTLY WITH LIGAND PRESENT IN REMARK 3 8AGA, PHB WAS MODELED WITH PARTIAL OCCUPANCY AND THE STRUCTURE REMARK 3 WAS REFINED USING 8AGA AS REFERENCE MODEL AND TLS = OFF. REMARK 4 REMARK 4 8WSV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300041931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : TUBE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.4.0 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14952 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 67.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.11600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.00 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: 8PQ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 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 47.61000 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 71.41500 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 23.80500 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 47.61000 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 23.80500 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 71.41500 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: 5450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13240 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 -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 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 394 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 ARG A 4 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 68 CG CD NE CZ NH1 NH2 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 VAL A 56 70.94 55.13 REMARK 500 ASP A 83 96.49 -161.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8PQ4 RELATED DB: PDB REMARK 900 HOSA APOPROTEIN REMARK 900 RELATED ID: 8AGA RELATED DB: PDB REMARK 900 HOSA WITH 4-HB LIGAND BOUND AT FIRST SITE REMARK 900 RELATED ID: 8KG0 RELATED DB: PDB REMARK 900 HOSA WITH 4-HB LIGAND BOUND AT SECOND SITE DBREF 8WSV A 1 135 UNP P69782 HOSA_ECO27 1 135 SEQADV 8WSV LEU A 136 UNP P69782 EXPRESSION TAG SEQADV 8WSV GLU A 137 UNP P69782 EXPRESSION TAG SEQADV 8WSV HIS A 138 UNP P69782 EXPRESSION TAG SEQADV 8WSV HIS A 139 UNP P69782 EXPRESSION TAG SEQADV 8WSV HIS A 140 UNP P69782 EXPRESSION TAG SEQADV 8WSV HIS A 141 UNP P69782 EXPRESSION TAG SEQADV 8WSV HIS A 142 UNP P69782 EXPRESSION TAG SEQADV 8WSV 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 HETNAM PHB P-HYDROXYBENZOIC ACID FORMUL 2 PHB C7 H6 O3 FORMUL 3 HOH *138(H2 O) HELIX 1 AA1 LYS A 6 LEU A 26 1 21 HELIX 2 AA2 THR A 30 LYS A 43 1 14 HELIX 3 AA3 GLN A 48 ALA A 55 1 8 HELIX 4 AA4 THR A 58 ARG A 72 1 15 HELIX 5 AA5 THR A 92 GLY A 115 1 24 HELIX 6 AA6 SER A 118 MET A 133 1 16 SHEET 1 AA1 3 ILE A 46 GLU A 47 0 SHEET 2 AA1 3 ASP A 83 LEU A 91 -1 O VAL A 89 N ILE A 46 SHEET 3 AA1 3 VAL A 75 ASP A 80 -1 N ARG A 76 O TRP A 90 CRYST1 67.470 67.470 95.220 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 0.014821 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010502 0.00000