HEADER SIGNALING PROTEIN 14-SEP-06 2ID9 TITLE 1.85 A STRUCTURE OF T87I/Y106W PHOSPHONO-CHEY COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHEMOTAXIS PROTEIN CHEY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CHEY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET24A(+)KAN+ KEYWDS ALPHA BETA PROTEIN FLAVODOXIN-LIKE TOPOLOGY ROSSMAN FOLD, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.J.HALKIDES,R.M.HAAS,K.A.MCADAMS,E.S.CASPER,B.D.SANTARSIERO, AUTHOR 2 A.D.MESECAR REVDAT 9 30-AUG-23 2ID9 1 REMARK REVDAT 8 26-JUL-23 2ID9 1 REMARK ATOM REVDAT 7 20-OCT-21 2ID9 1 SEQADV LINK REVDAT 6 18-OCT-17 2ID9 1 REMARK REVDAT 5 28-MAY-14 2ID9 1 REMARK VERSN REVDAT 4 09-JUN-09 2ID9 1 REVDAT REVDAT 3 24-FEB-09 2ID9 1 VERSN REVDAT 2 02-DEC-08 2ID9 1 JRNL REVDAT 1 25-SEP-07 2ID9 0 JRNL AUTH K.MCADAMS,E.S.CASPER,R.MATTHEW HAAS,B.D.SANTARSIERO, JRNL AUTH 2 A.L.EGGLER,A.MESECAR,C.J.HALKIDES JRNL TITL THE STRUCTURES OF T87I PHOSPHONO-CHEY AND T87I/Y106W JRNL TITL 2 PHOSPHONO-CHEY HELP TO EXPLAIN THEIR BINDING AFFINITIES TO JRNL TITL 3 THE FLIM AND CHEZ PEPTIDES. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 479 105 2008 JRNL REFN ISSN 0003-9861 JRNL PMID 18801331 JRNL DOI 10.1016/J.ABB.2008.08.019 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 10988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 569 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2421 REMARK 3 BIN FREE R VALUE : 0.3118 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 418 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 985 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07700 REMARK 3 B22 (A**2) : -0.28000 REMARK 3 B33 (A**2) : 0.20300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.430 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 50.91 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NEWPROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ID9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.84 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11203 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1C4W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.2 M AMMONIUM ACETATE, REMARK 280 0.1 M MES-NAOH, PH 5.84, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.0K 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 20.67500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.67500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.98000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CH2 TRP A 106 O HOH A 201 3745 1.43 REMARK 500 OG1 THR A 16 OD2 ASP A 75 2674 1.67 REMARK 500 CZ2 TRP A 106 O HOH A 201 3745 1.83 REMARK 500 CD LYS A 92 O HOH A 154 1655 1.86 REMARK 500 OD1 ASN A 62 CH2 TRP A 106 3755 2.15 REMARK 500 OD1 ASN A 62 CZ2 TRP A 106 3755 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 4 27.24 -74.32 REMARK 500 ASN A 62 -72.78 75.11 REMARK 500 MET A 78 24.12 -147.13 REMARK 500 LEU A 127 17.56 -68.39 REMARK 500 LEU A 127 17.56 -69.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C4W RELATED DB: PDB REMARK 900 1.9 A STRUCTURE OF A-THIOPHOSPHONATE MODIFIED CHEY D57C DBREF 2ID9 A 2 129 UNP P0AE67 CHEY_ECOLI 1 128 SEQADV 2ID9 CYQ A 57 UNP P0AE67 ASP 56 ENGINEERED MUTATION SEQADV 2ID9 ILE A 87 UNP P0AE67 THR 86 ENGINEERED MUTATION SEQADV 2ID9 TRP A 106 UNP P0AE67 TYR 105 ENGINEERED MUTATION SEQRES 1 A 128 ALA ASP LYS GLU LEU LYS PHE LEU VAL VAL ASP ASP PHE SEQRES 2 A 128 SER THR MET ARG ARG ILE VAL ARG ASN LEU LEU LYS GLU SEQRES 3 A 128 LEU GLY PHE ASN ASN VAL GLU GLU ALA GLU ASP GLY VAL SEQRES 4 A 128 ASP ALA LEU ASN LYS LEU GLN ALA GLY GLY TYR GLY PHE SEQRES 5 A 128 VAL ILE SER CYQ TRP ASN MET PRO ASN MET ASP GLY LEU SEQRES 6 A 128 GLU LEU LEU LYS THR ILE ARG ALA ASP GLY ALA MET SER SEQRES 7 A 128 ALA LEU PRO VAL LEU MET VAL ILE ALA GLU ALA LYS LYS SEQRES 8 A 128 GLU ASN ILE ILE ALA ALA ALA GLN ALA GLY ALA SER GLY SEQRES 9 A 128 TRP VAL VAL LYS PRO PHE THR ALA ALA THR LEU GLU GLU SEQRES 10 A 128 LYS LEU ASN LYS ILE PHE GLU LYS LEU GLY MET MODRES 2ID9 CYQ A 57 CYS HET CYQ A 57 11 HETNAM CYQ 2-AMINO-3-PHOSPHONOMETHYLSULFANYL-PROPIONIC ACID HETSYN CYQ S-METHYL PHOSPHOCYSTEINE FORMUL 1 CYQ C4 H10 N O5 P S FORMUL 2 HOH *79(H2 O) HELIX 1 1 PHE A 14 LEU A 28 1 15 HELIX 2 2 ASP A 38 ALA A 48 1 11 HELIX 3 3 ASP A 64 ALA A 74 1 11 HELIX 4 4 LYS A 91 ALA A 101 1 11 HELIX 5 5 THR A 112 LEU A 127 1 16 SHEET 1 A 5 VAL A 33 ALA A 36 0 SHEET 2 A 5 PHE A 8 VAL A 11 1 N PHE A 8 O GLU A 34 SHEET 3 A 5 PHE A 53 CYQ A 57 1 O ILE A 55 N LEU A 9 SHEET 4 A 5 VAL A 83 ILE A 87 1 O LEU A 84 N VAL A 54 SHEET 5 A 5 GLY A 105 VAL A 108 1 O VAL A 107 N ILE A 87 LINK C SER A 56 N CYQ A 57 1555 1555 1.33 LINK C CYQ A 57 N TRP A 58 1555 1555 1.33 CISPEP 1 LYS A 109 PRO A 110 0 0.81 CRYST1 41.350 49.960 53.900 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 0.024184 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018553 0.00000