HEADER SIGNALING PROTEIN 09-DEC-15 5B1O TITLE DHP DOMAIN STRUCTURE OF ENVZ P248A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: OSMOLARITY SENSOR PROTEIN ENVZ; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DHP DOMAIN, UNP RESIDUES 223-289; COMPND 5 EC: 2.7.13.3,2.7.3.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ENVZ; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TWO-COMPONENT SYSTEM, AUTOPHOSPHORYLATION, DHP DOMAIN, HISTIDINE KEYWDS 2 KINASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.OKAJIMA,Y.EGUCHI,N.TOCHIO,Y.INUKAI,R.SHIMIZU,S.UEDA,S.SHINYA, AUTHOR 2 T.KIGAWA,T.FUKAMIZO,M.IGARASHI,R.UTSUMI REVDAT 4 08-NOV-23 5B1O 1 REMARK REVDAT 3 25-DEC-19 5B1O 1 REMARK REVDAT 2 29-MAR-17 5B1O 1 JRNL REVDAT 1 14-DEC-16 5B1O 0 JRNL AUTH Y.EGUCHI,T.OKAJIMA,N.TOCHIO,Y.INUKAI,R.SHIMIZU,S.UEDA, JRNL AUTH 2 S.SHINYA,T.KIGAWA,T.FUKAMIZO,M.IGARASHI,R.UTSUMI JRNL TITL ANGUCYCLINE ANTIBIOTIC WALDIOMYCIN RECOGNIZES COMMON JRNL TITL 2 STRUCTURAL MOTIF CONSERVED IN BACTERIAL HISTIDINE KINASES JRNL REF J. ANTIBIOT. V. 70 251 2017 JRNL REFN ISSN 0021-8820 JRNL PMID 27999439 JRNL DOI 10.1038/JA.2016.151 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 6909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.760 REMARK 3 FREE R VALUE TEST SET COUNT : 427 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 3.2138 - 2.5524 1.00 2328 143 0.2873 0.3336 REMARK 3 2 2.5524 - 2.2302 0.98 2245 141 0.3028 0.3367 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.27 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 : 0.013 971 REMARK 3 ANGLE : 1.297 1306 REMARK 3 CHIRALITY : 0.060 156 REMARK 3 PLANARITY : 0.006 172 REMARK 3 DIHEDRAL : 15.959 372 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 5B1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1300000370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SCALA REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7507 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 63.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : 0.24900 REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.5 REMARK 200 STARTING MODEL: 5B1N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM FORMATE, 15% PEG 3350, REMARK 280 PH 6.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.74933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 127.49867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 127.49867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.74933 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: 2380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 221 REMARK 465 TYR A 287 REMARK 465 LEU A 288 REMARK 465 ARG A 289 REMARK 465 GLY B 221 REMARK 465 ALA B 222 REMARK 465 MET B 223 REMARK 465 ALA B 224 REMARK 465 ALA B 225 REMARK 465 GLY B 226 REMARK 465 VAL B 227 REMARK 465 LYS B 228 REMARK 465 TYR B 287 REMARK 465 LEU B 288 REMARK 465 ARG B 289 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 ALA B 231 -75.75 -122.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B1N RELATED DB: PDB DBREF1 5B1O A 223 289 UNP A0A0K5ZMN4_ECOLX DBREF2 5B1O A A0A0K5ZMN4 223 289 DBREF1 5B1O B 223 289 UNP A0A0K5ZMN4_ECOLX DBREF2 5B1O B A0A0K5ZMN4 223 289 SEQADV 5B1O GLY A 221 UNP A0A0K5ZMN EXPRESSION TAG SEQADV 5B1O ALA A 222 UNP A0A0K5ZMN EXPRESSION TAG SEQADV 5B1O ALA A 248 UNP A0A0K5ZMN PRO 248 ENGINEERED MUTATION SEQADV 5B1O GLY B 221 UNP A0A0K5ZMN EXPRESSION TAG SEQADV 5B1O ALA B 222 UNP A0A0K5ZMN EXPRESSION TAG SEQADV 5B1O ALA B 248 UNP A0A0K5ZMN PRO 248 ENGINEERED MUTATION SEQRES 1 A 69 GLY ALA MET ALA ALA GLY VAL LYS GLN LEU ALA ASP ASP SEQRES 2 A 69 ARG THR LEU LEU MET ALA GLY VAL SER HIS ASP LEU ARG SEQRES 3 A 69 THR ALA LEU THR ARG ILE ARG LEU ALA THR GLU MET MET SEQRES 4 A 69 SER GLU GLN ASP GLY TYR LEU ALA GLU SER ILE ASN LYS SEQRES 5 A 69 ASP ILE GLU GLU CYS ASN ALA ILE ILE GLU GLN PHE ILE SEQRES 6 A 69 ASP TYR LEU ARG SEQRES 1 B 69 GLY ALA MET ALA ALA GLY VAL LYS GLN LEU ALA ASP ASP SEQRES 2 B 69 ARG THR LEU LEU MET ALA GLY VAL SER HIS ASP LEU ARG SEQRES 3 B 69 THR ALA LEU THR ARG ILE ARG LEU ALA THR GLU MET MET SEQRES 4 B 69 SER GLU GLN ASP GLY TYR LEU ALA GLU SER ILE ASN LYS SEQRES 5 B 69 ASP ILE GLU GLU CYS ASN ALA ILE ILE GLU GLN PHE ILE SEQRES 6 B 69 ASP TYR LEU ARG FORMUL 3 HOH *28(H2 O) HELIX 1 AA1 GLY A 226 ASP A 232 1 7 HELIX 2 AA2 ARG A 234 MET A 258 1 25 HELIX 3 AA3 SER A 260 GLN A 262 5 3 HELIX 4 AA4 ASP A 263 ILE A 285 1 23 HELIX 5 AA5 ALA B 231 GLU B 257 1 27 HELIX 6 AA6 ASP B 263 ILE B 285 1 23 CRYST1 35.761 35.761 191.248 90.00 90.00 120.00 P 31 2 1 12 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 0.027964 0.016145 0.000000 0.00000 SCALE2 0.000000 0.032290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005229 0.00000