HEADER SIGNALING PROTEIN 15-SEP-06 2IDM
TITLE 2.00 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 7 30-AUG-23 2IDM 1 REMARK
REVDAT 6 20-OCT-21 2IDM 1 REMARK SEQADV LINK
REVDAT 5 18-OCT-17 2IDM 1 REMARK
REVDAT 4 09-JUN-09 2IDM 1 REVDAT
REVDAT 3 24-FEB-09 2IDM 1 VERSN
REVDAT 2 02-DEC-08 2IDM 1 JRNL
REVDAT 1 25-SEP-07 2IDM 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. 2.00 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) : 2.00
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) (%) : 88.5
REMARK 3 NUMBER OF REFLECTIONS : 6780
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) : 0.233
REMARK 3 FREE R VALUE : 0.328
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 378
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) : 2.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.50
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2333
REMARK 3 BIN FREE R VALUE : 0.3283
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 378
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 : 4
REMARK 3 SOLVENT ATOMS : 100
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.45
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -17.09600
REMARK 3 B22 (A**2) : -4.55500
REMARK 3 B33 (A**2) : 21.65200
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) : 1.381
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 : 87.78
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 : ACE.PARAM
REMARK 3 PARAMETER FILE 5 : 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 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2IDM 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_1000039451.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-JUL-02
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.88
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 : 6822
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 99.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 88.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.07300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03
REMARK 200 COMPLETENESS FOR SHELL (%) : 62.7
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.44300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 1C4W
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 35.35
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.2M AMMONIUM ACETATE,
REMARK 280 0.1 M MES-NAOH, PH 5.88, 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 20.04550
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.47800
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.27200
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.47800
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.04550
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.27200
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: 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 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 NH1 ARG A 19 O HOH A 233 2.13
REMARK 500
REMARK 500 REMARK: NULL
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 O HOH A 231 O HOH A 254 1655 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 PHE A 53 136.24 -175.62
REMARK 500 ASN A 62 -81.67 83.00
REMARK 500 GLU A 93 -70.84 -53.55
REMARK 500 LEU A 127 -13.86 -49.79
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 201
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 2IDM A 2 129 UNP P0AE67 CHEY_ECOLI 1 128
SEQADV 2IDM CYQ A 57 UNP P0AE67 ASP 56 ENGINEERED MUTATION
SEQADV 2IDM ILE A 87 UNP P0AE67 THR 86 ENGINEERED MUTATION
SEQADV 2IDM 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 2IDM CYQ A 57 CYS
HET CYQ A 57 11
HET ACT A 201 4
HETNAM CYQ 2-AMINO-3-PHOSPHONOMETHYLSULFANYL-PROPIONIC ACID
HETNAM ACT ACETATE ION
HETSYN CYQ S-METHYL PHOSPHOCYSTEINE
FORMUL 1 CYQ C4 H10 N O5 P S
FORMUL 2 ACT C2 H3 O2 1-
FORMUL 3 HOH *100(H2 O)
HELIX 1 1 PHE A 14 GLY A 29 1 16
HELIX 2 2 ASP A 38 GLN A 47 1 10
HELIX 3 3 ASP A 64 ASP A 75 1 12
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 VAL A 10 O ALA A 36
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 1.32
LINK C CYQ A 57 N TRP A 58 1555 1555 1.31
CISPEP 1 LYS A 109 PRO A 110 0 -0.07
SITE 1 AC1 4 TRP A 58 ASN A 59 ASN A 94 HOH A 257
CRYST1 40.091 50.544 52.956 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 0.024943 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019785 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018884 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
