HEADER SIGNALING PROTEIN 09-DEC-15 5B1N TITLE DHP DOMAIN STRUCTURE OF ENVZ FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: OSMOLARITY SENSOR PROTEIN ENVZ; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DHP DOMAIN, UNP RESIDUES 223-289; COMPND 5 EC: 2.7.13.3,2.7.3.-; COMPND 6 ENGINEERED: 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 5B1N 1 REMARK REVDAT 3 26-FEB-20 5B1N 1 REMARK REVDAT 2 29-MAR-17 5B1N 1 JRNL REVDAT 1 14-DEC-16 5B1N 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. 1.33 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 15904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 817 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 2.4157 - 1.9180 1.00 2556 152 0.1765 0.1971 REMARK 3 2 1.9180 - 1.6757 1.00 2585 125 0.1805 0.2010 REMARK 3 3 1.6757 - 1.5226 1.00 2579 133 0.1732 0.2144 REMARK 3 4 1.5226 - 1.4135 0.99 2551 139 0.1917 0.2305 REMARK 3 5 1.4135 - 1.3302 1.00 2554 139 0.2154 0.2500 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.11 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 : 0.016 488 REMARK 3 ANGLE : 1.623 658 REMARK 3 CHIRALITY : 0.070 76 REMARK 3 PLANARITY : 0.009 87 REMARK 3 DIHEDRAL : 14.214 191 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): 10.3423 22.1493 -0.1481 REMARK 3 T TENSOR REMARK 3 T11: 0.1253 T22: 0.0968 REMARK 3 T33: 0.1961 T12: 0.0330 REMARK 3 T13: 0.0031 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 2.5784 L22: 1.5465 REMARK 3 L33: 4.9040 L12: -0.3843 REMARK 3 L13: 0.1373 L23: -0.6642 REMARK 3 S TENSOR REMARK 3 S11: 0.0965 S12: 0.1145 S13: 0.1425 REMARK 3 S21: -0.1728 S22: -0.1784 S23: -0.0440 REMARK 3 S31: -0.2228 S32: 0.1106 S33: 0.0714 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 5B1N 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_1300000369. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-14 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 : 15966 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 42.258 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 18.1000 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) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41800 REMARK 200 R SYM FOR SHELL (I) : 0.41800 REMARK 200 FOR SHELL : 1.800 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: 3ZRX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1-1.3 M SODIUM/POTASSIUM PHOSPHATE, 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 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,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 56.33867 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 28.16933 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.33867 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 28.16933 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: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 19.25500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 33.35064 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 GLY A 221 REMARK 465 ALA A 222 REMARK 465 MET A 223 REMARK 465 ALA A 224 REMARK 465 ALA A 225 REMARK 465 GLY A 226 REMARK 465 VAL A 227 REMARK 465 LYS A 228 REMARK 465 GLN A 229 REMARK 465 LEU A 230 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 275 O HOH A 301 1.91 REMARK 500 O HOH A 320 O HOH A 345 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 392 DISTANCE = 7.09 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B1O RELATED DB: PDB DBREF1 5B1N A 223 289 UNP A0A0K5ZMN4_ECOLX DBREF2 5B1N A A0A0K5ZMN4 223 289 SEQADV 5B1N GLY A 221 UNP A0A0K5ZMN EXPRESSION TAG SEQADV 5B1N ALA A 222 UNP A0A0K5ZMN EXPRESSION TAG 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 PRO 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 FORMUL 2 HOH *92(H2 O) HELIX 1 AA1 ASP A 233 GLU A 257 1 25 HELIX 2 AA2 MET A 258 MET A 259 5 2 HELIX 3 AA3 SER A 260 GLN A 262 5 3 HELIX 4 AA4 ASP A 263 LEU A 288 1 26 CRYST1 38.510 38.510 84.508 90.00 90.00 120.00 P 62 6 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 0.025968 0.014992 0.000000 0.00000 SCALE2 0.000000 0.029985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011833 0.00000