HEADER SIGNALING PROTEIN 13-SEP-00 1FU0 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE PHOSPHO-SERINE 46 HPR FROM TITLE 2 ENTEROCOCCUS FAECALIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOCARRIER PROTEIN HPR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HISTIDINE-CONTAINING PROTEIN, HISTIDINE-CONTAINING COMPND 5 PHOSPHOCARRIER PROTEIN, HPR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 STRAIN: 26487 KEYWDS PHOSPHO-SERINE HPR, PTS SYSTEM, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.F.AUDETTE,R.ENGELMANN,W.HENGSTENBERG,J.DEUTSCHER,K.HAYAKAWA, AUTHOR 2 J.W.QUAIL,L.T.J.DELBAERE REVDAT 4 21-DEC-22 1FU0 1 SEQADV LINK REVDAT 3 24-FEB-09 1FU0 1 VERSN REVDAT 2 01-APR-03 1FU0 1 JRNL REVDAT 1 22-NOV-00 1FU0 0 JRNL AUTH G.F.AUDETTE,R.ENGELMANN,W.HENGSTENBERG,J.DEUTSCHER, JRNL AUTH 2 K.HAYAKAWA,J.W.QUAIL,L.T.DELBAERE JRNL TITL THE 1.9 A RESOLUTION STRUCTURE OF PHOSPHO-SERINE 46 HPR FROM JRNL TITL 2 ENTEROCOCCUS FAECALIS. JRNL REF J.MOL.BIOL. V. 303 545 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11054290 JRNL DOI 10.1006/JMBI.2000.4166 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 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) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 10043 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) : 0.178 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 496 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 : 1292 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.590 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.93 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.150 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 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: SIMULATED ANNEALING REMARK 4 REMARK 4 1FU0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1000011898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 290.0 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 4.230 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.11000 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M SODIUM-POTASSIUM PHOSPHATE, PH REMARK 280 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 21.60000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A 16 -141.76 57.65 REMARK 500 ALA B 116 -154.30 63.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PTF RELATED DB: PDB REMARK 900 THE NATIVE HPR FROM ENTEROCOCCUS FAECALIS DBREF 1FU0 A 1 87 UNP P07515 PTHP_ENTFA 1 87 DBREF 1FU0 B 101 187 UNP P07515 PTHP_ENTFA 1 87 SEQADV 1FU0 SEP A 46 UNP P07515 SER 46 MODIFIED RESIDUE SEQADV 1FU0 SEP B 146 UNP P07515 SER 46 MODIFIED RESIDUE SEQRES 1 A 87 MET GLU LYS LYS GLU PHE HIS ILE VAL ALA GLU THR GLY SEQRES 2 A 87 ILE HIS ALA ARG PRO ALA THR LEU LEU VAL GLN THR ALA SEQRES 3 A 87 SER LYS PHE ASN SER ASP ILE ASN LEU GLU TYR LYS GLY SEQRES 4 A 87 LYS SER VAL ASN LEU LYS SEP ILE MET GLY VAL MET SER SEQRES 5 A 87 LEU GLY VAL GLY GLN GLY SER ASP VAL THR ILE THR VAL SEQRES 6 A 87 ASP GLY ALA ASP GLU ALA GLU GLY MET ALA ALA ILE VAL SEQRES 7 A 87 GLU THR LEU GLN LYS GLU GLY LEU ALA SEQRES 1 B 87 MET GLU LYS LYS GLU PHE HIS ILE VAL ALA GLU THR GLY SEQRES 2 B 87 ILE HIS ALA ARG PRO ALA THR LEU LEU VAL GLN THR ALA SEQRES 3 B 87 SER LYS PHE ASN SER ASP ILE ASN LEU GLU TYR LYS GLY SEQRES 4 B 87 LYS SER VAL ASN LEU LYS SEP ILE MET GLY VAL MET SER SEQRES 5 B 87 LEU GLY VAL GLY GLN GLY SER ASP VAL THR ILE THR VAL SEQRES 6 B 87 ASP GLY ALA ASP GLU ALA GLU GLY MET ALA ALA ILE VAL SEQRES 7 B 87 GLU THR LEU GLN LYS GLU GLY LEU ALA MODRES 1FU0 SEP A 46 SER PHOSPHOSERINE MODRES 1FU0 SEP B 146 SER PHOSPHOSERINE HET SEP A 46 10 HET SEP B 146 10 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 3 HOH *91(H2 O) HELIX 1 1 HIS A 15 LYS A 28 1 14 HELIX 2 2 ILE A 47 GLY A 54 1 8 HELIX 3 3 ASP A 69 GLU A 84 1 16 HELIX 4 4 HIS B 115 LYS B 128 1 14 HELIX 5 5 ILE B 147 GLY B 154 1 8 HELIX 6 6 ASP B 169 GLU B 184 1 16 SHEET 1 A 4 GLU A 2 HIS A 7 0 SHEET 2 A 4 ASP A 60 ASP A 66 -1 O VAL A 61 N PHE A 6 SHEET 3 A 4 ASP A 32 TYR A 37 -1 N ASP A 32 O ASP A 66 SHEET 4 A 4 LYS A 40 ASN A 43 -1 O LYS A 40 N TYR A 37 SHEET 1 B 4 GLU B 102 HIS B 107 0 SHEET 2 B 4 ASP B 160 ASP B 166 -1 O VAL B 161 N PHE B 106 SHEET 3 B 4 ASP B 132 TYR B 137 -1 N ASP B 132 O ASP B 166 SHEET 4 B 4 LYS B 140 ASN B 143 -1 O LYS B 140 N TYR B 137 LINK C LYS A 45 N SEP A 46 1555 1555 1.33 LINK C SEP A 46 N ILE A 47 1555 1555 1.33 LINK C LYS B 145 N SEP B 146 1555 1555 1.33 LINK C SEP B 146 N ILE B 147 1555 1555 1.32 CRYST1 25.520 43.200 60.750 90.00 92.67 90.00 P 1 21 1 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 0.039180 0.000000 0.001830 0.00000 SCALE2 0.000000 0.023150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016480 0.00000 MTRIX1 1 -0.998720 0.020550 0.046230 11.08700 1 MTRIX2 1 0.015950 0.995090 -0.097690 -23.54104 1 MTRIX3 1 -0.048010 -0.096820 -0.994140 32.35572 1