HEADER TRANSCRIPTION REGULATOR 28-OCT-05 2EUB OBSLTE 22-MAY-07 2EUB 2PL1 TITLE E.COLI PHOP RECEIVER DOMAIN ACTIVATED WITH BEF3- COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATORY PROTEIN PHOP; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL RECEIVER DOMAIN (RESIDUES 1-121); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 GENE: PHOP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PJES307; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PEF31 KEYWDS CHEY-LIKE FOLD, RESPONSE REGULATOR, BERYLLIUM FLUORIDE, KEYWDS 2 TRANSCRIPTION FACTOR, PHOP, ACTIVATED, VIRULENCE EXPDTA X-RAY DIFFRACTION AUTHOR P.BACHHAWAT,A.M.STOCK REVDAT 2 22-MAY-07 2EUB 1 OBSLTE REVDAT 1 31-OCT-06 2EUB 0 JRNL AUTH P.BACHHAWAT,A.M.STOCK JRNL TITL CRYSTAL STRUCTURES OF UNACTIVATED AND ACTIVE JRNL TITL 2 RECEIVER DOMAINS OF E.COLI PHOP SUGGEST A JRNL TITL 3 MECHANISM OF ACTIVATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 28906 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2803 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 969 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.17 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 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : MAXIMUM LIKELIHOOD 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 : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EUB COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-2005. REMARK 100 THE RCSB ID CODE IS RCSB035101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-2004 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.90 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0714 REMARK 200 MONOCHROMATOR : KOHZU DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR WITH A REMARK 200 SAGITTALLY FOCUSED SECOND REMARK 200 CRYSTAL. CRYSTAL TYPE SI(111) REMARK 200 OPTICS : SPHERICAL MIRRORS 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 : 34549 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.00000 REMARK 200 R SYM (I) : 0.11900 REMARK 200 FOR THE DATA SET : 10.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.68000 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM THIOCYANATE, PEG3350, PH REMARK 280 6.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,1/3+Z REMARK 290 3555 -X+Y,-X,2/3+Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,1/3+Z REMARK 290 6555 X-Y,X,2/3+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 -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 10.33800 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 20.67600 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 10.33800 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 20.67600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 -154.68750 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -89.30887 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH 101 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 26 CG CD OE1 NE2 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 REMARK 500 OD1 ASP A 51 BE BEF 201 1.94 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EU6 RELATED DB: PDB REMARK 900 RECEIVER DOMAIN OF PHOP UNACTIVATED DBREF 2EUB A 1 121 UNP P23836 PHOP_ECOLI 1 121 SEQADV 2EUB MSE A 1 UNP P23836 MET 1 MODIFIED RESIDUE SEQADV 2EUB MSE A 109 UNP P23836 MET 109 MODIFIED RESIDUE SEQADV 2EUB MSE A 112 UNP P23836 MET 112 MODIFIED RESIDUE SEQADV 2EUB MSE A 116 UNP P23836 MET 116 MODIFIED RESIDUE SEQADV 2EUB GLN A 121 UNP P23836 GLY 121 ENGINEERED SEQRES 1 A 121 MSE ARG VAL LEU VAL VAL GLU ASP ASN ALA LEU LEU ARG SEQRES 2 A 121 HIS HIS LEU LYS VAL GLN ILE GLN ASP ALA GLY HIS GLN SEQRES 3 A 121 VAL ASP ASP ALA GLU ASP ALA LYS GLU ALA ASP TYR TYR SEQRES 4 A 121 LEU ASN GLU HIS ILE PRO ASP ILE ALA ILE VAL ASP LEU SEQRES 5 A 121 GLY LEU PRO ASP GLU ASP GLY LEU SER LEU ILE ARG ARG SEQRES 6 A 121 TRP ARG SER ASN ASP VAL SER LEU PRO ILE LEU VAL LEU SEQRES 7 A 121 THR ALA ARG GLU SER TRP GLN ASP LYS VAL GLU VAL LEU SEQRES 8 A 121 SER ALA GLY ALA ASP ASP TYR VAL THR LYS PRO PHE HIS SEQRES 9 A 121 ILE GLU GLU VAL MSE ALA ARG MSE GLN ALA LEU MSE ARG SEQRES 10 A 121 ARG ASN SER GLN MODRES 2EUB MSE A 1 MET SELENOMETHIONINE MODRES 2EUB MSE A 109 MET SELENOMETHIONINE MODRES 2EUB MSE A 112 MET SELENOMETHIONINE MODRES 2EUB MSE A 116 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 109 8 HET MSE A 112 8 HET MSE A 116 8 HET PT 301 1 HET PT 302 1 HET PT 303 1 HET MG 401 1 HET BEF 201 4 HETNAM MSE SELENOMETHIONINE HETNAM PT PLATINUM (II) ION HETNAM MG MAGNESIUM ION HETNAM BEF BERYLLIUM TRIFLUORIDE ION FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 PT 3(PT 2+) FORMUL 5 MG MG 2+ FORMUL 6 BEF BE F3 1- FORMUL 7 HOH *111(H2 O) HELIX 1 1 ASN A 9 ALA A 23 1 15 HELIX 2 2 ASP A 32 HIS A 43 1 12 HELIX 3 3 ASP A 58 ASN A 69 1 12 HELIX 4 4 SER A 83 ALA A 93 1 11 HELIX 5 5 HIS A 104 SER A 120 1 17 SHEET 1 A 5 GLN A 26 ALA A 30 0 SHEET 2 A 5 ARG A 2 VAL A 6 1 N VAL A 5 O ALA A 30 SHEET 3 A 5 ILE A 47 VAL A 50 1 O ILE A 49 N LEU A 4 SHEET 4 A 5 ILE A 75 THR A 79 1 O LEU A 76 N ALA A 48 SHEET 5 A 5 ASP A 97 THR A 100 1 O VAL A 99 N VAL A 77 CISPEP 1 LYS A 101 PRO A 102 0 -0.26 CRYST1 103.125 103.125 31.014 90.00 90.00 120.00 P 64 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 0.009697 0.005599 0.000000 0.00000 SCALE2 0.000000 0.011197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032244 0.00000 HETATM 1 N MSE A 1 -61.096 -44.143 -12.827 1.00 50.10 N HETATM 2 CA MSE A 1 -61.767 -43.848 -11.531 1.00 48.59 C HETATM 3 C MSE A 1 -61.067 -42.712 -10.785 1.00 44.53 C HETATM 4 O MSE A 1 -60.016 -42.908 -10.171 1.00 43.68 O HETATM 5 CB MSE A 1 -61.790 -45.104 -10.652 1.00 55.17 C HETATM 6 CG MSE A 1 -62.654 -46.246 -11.189 1.00 62.75 C HETATM 7 SE MSE A 1 -64.552 -45.839 -11.237 1.00 75.69 SE HETATM 8 CE MSE A 1 -64.692 -45.264 -13.081 1.00 69.51 C