HEADER TRANSFERASE 28-JUN-23 8JWD TITLE HISTIDINE KINASE QSEE SENSOR DOMAIN OF ESCHERICHIA COLI O157:H7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: QUORUM-SENSING REGULATOR PROTEIN E; COMPND 5 EC: 2.7.13.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O157:H7; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 GENE: QSEE, C2R31_001944, HEP34_004735; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ENTEROHEMORRHAGIC ESCHERICHIA COLI, TWO-COMPONENT SYSTEMS, INNER KEYWDS 2 MEMBRANE PROTEIN, SIGNALING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.MATSUMOTO,Y.FUKUDA,T.INOUE REVDAT 1 15-NOV-23 8JWD 0 JRNL AUTH K.MATSUMOTO,Y.FUKUDA,T.INOUE JRNL TITL CRYSTAL STRUCTURES OF QSEE AND QSEG: ELEMENTS OF A JRNL TITL 2 THREE-COMPONENT SYSTEM FROM ESCHERICHIA COLI. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 79 285 2023 JRNL REFN ESSN 2053-230X JRNL PMID 37877621 JRNL DOI 10.1107/S2053230X23009123 REMARK 2 REMARK 2 RESOLUTION. 1.33 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 25667 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1296 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 43.5000 - 2.7700 1.00 2943 146 0.1623 0.1927 REMARK 3 2 2.7700 - 2.2000 1.00 2769 137 0.1482 0.1503 REMARK 3 3 2.2000 - 1.9200 1.00 2760 145 0.1286 0.1673 REMARK 3 4 1.9200 - 1.7400 0.99 2675 160 0.1277 0.1625 REMARK 3 5 1.7400 - 1.6200 0.99 2703 148 0.1212 0.1500 REMARK 3 6 1.6200 - 1.5200 0.99 2661 140 0.1200 0.1699 REMARK 3 7 1.5200 - 1.4500 0.98 2666 132 0.1162 0.1615 REMARK 3 8 1.4500 - 1.3800 0.98 2641 148 0.1426 0.2184 REMARK 3 9 1.3800 - 1.3300 0.95 2553 140 0.1755 0.2524 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) : 0.144 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.318 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.08 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 : 0.005 1066 REMARK 3 ANGLE : 0.859 1451 REMARK 3 CHIRALITY : 0.074 162 REMARK 3 PLANARITY : 0.009 199 REMARK 3 DIHEDRAL : 5.182 161 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 8JWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300036519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 1.12.14 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25729 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 43.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 18.90 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.68000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M SODIUM FORMATE, 0.1 M HEPES PH REMARK 280 7.2, 18% (W/V) POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 15.94250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.49850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.73950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.49850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.94250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.73950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 20 REMARK 465 GLY A 21 REMARK 465 SER A 22 REMARK 465 SER A 23 REMARK 465 HIS A 24 REMARK 465 HIS A 25 REMARK 465 HIS A 26 REMARK 465 HIS A 27 REMARK 465 HIS A 28 REMARK 465 HIS A 29 REMARK 465 GLY A 30 REMARK 465 GLY A 31 REMARK 465 GLY A 32 REMARK 465 SER A 33 REMARK 465 GLU A 34 REMARK 465 ASN A 35 REMARK 465 LEU A 36 REMARK 465 TYR A 37 REMARK 465 PHE A 38 REMARK 465 GLN A 39 REMARK 465 GLY A 40 REMARK 465 SER A 41 REMARK 465 ASP A 42 REMARK 465 GLN A 43 REMARK 465 GLU A 167 DBREF1 8JWD A 41 167 UNP A0A2T3SYV0_ECOLX DBREF2 8JWD A A0A2T3SYV0 41 167 SEQADV 8JWD MET A 20 UNP A0A2T3SYV INITIATING METHIONINE SEQADV 8JWD GLY A 21 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD SER A 22 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD SER A 23 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD HIS A 24 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD HIS A 25 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD HIS A 26 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD HIS A 27 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD HIS A 28 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD HIS A 29 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD GLY A 30 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD GLY A 31 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD GLY A 32 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD SER A 33 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD GLU A 34 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD ASN A 35 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD LEU A 36 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD TYR A 37 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD PHE A 38 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD GLN A 39 UNP A0A2T3SYV EXPRESSION TAG SEQADV 8JWD GLY A 40 UNP A0A2T3SYV EXPRESSION TAG SEQRES 1 A 148 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLY GLY GLY SEQRES 2 A 148 SER GLU ASN LEU TYR PHE GLN GLY SER ASP GLN ALA ALA SEQRES 3 A 148 LEU VAL ASN ARG THR THR LEU ILE ASP ALA ARG ARG SER SEQRES 4 A 148 GLU ALA MET THR ASN ALA ALA LEU GLU MET GLU ARG SER SEQRES 5 A 148 TYR ARG GLN TYR CYS VAL LEU ASP ASP PRO THR LEU ALA SEQRES 6 A 148 LYS VAL TYR GLN SER GLN ARG LYS ARG TYR SER GLU MET SEQRES 7 A 148 LEU ASP ALA HIS ALA GLY VAL LEU PRO ASP ASP LYS LEU SEQRES 8 A 148 TYR GLN ALA LEU ARG GLN ASP LEU ASN ASN LEU ALA GLN SEQRES 9 A 148 LEU GLN CYS ASN ASN SER GLY PRO ASP ALA ALA ALA ALA SEQRES 10 A 148 ALA ARG LEU GLU ALA PHE ALA SER ALA ASN THR GLU MET SEQRES 11 A 148 VAL GLN ALA THR ARG THR VAL VAL PHE SER ARG GLY GLN SEQRES 12 A 148 GLN LEU GLN ARG GLU HET EDO A 201 8 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 HOH *128(H2 O) HELIX 1 AA1 ALA A 44 ASP A 79 1 36 HELIX 2 AA2 THR A 82 ALA A 102 1 21 HELIX 3 AA3 ASP A 108 ASN A 120 1 13 HELIX 4 AA4 ASP A 132 ARG A 160 1 29 SSBOND 1 CYS A 76 CYS A 126 1555 1555 2.07 CRYST1 31.885 39.479 86.997 90.00 90.00 90.00 P 21 21 21 4 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 0.031363 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011495 0.00000