HEADER SIGNALING PROTEIN 10-JUN-04 1TM2 TITLE CRYSTAL STRUCTURE OF THE APO FORM OF THE SALMONELLA TYPHIMURIUM AI-2 TITLE 2 RECEPTOR LSRB COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUGAR TRANSPORT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 99287; SOURCE 4 STRAIN: LT2; SOURCE 5 GENE: LSRB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 KEYWDS PERIPLASMIC BINDING PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.T.MILLER,K.B.XAVIER,S.R.CAMPAGNA,M.E.TAGA,M.F.SEMMELHACK, AUTHOR 2 B.L.BASSLER,F.M.HUGHSON REVDAT 5 06-NOV-24 1TM2 1 SEQADV REVDAT 4 31-JAN-18 1TM2 1 REMARK REVDAT 3 13-JUL-11 1TM2 1 VERSN REVDAT 2 24-FEB-09 1TM2 1 VERSN REVDAT 1 28-SEP-04 1TM2 0 JRNL AUTH S.T.MILLER,K.B.XAVIER,S.R.CAMPAGNA,M.E.TAGA,M.F.SEMMELHACK, JRNL AUTH 2 B.L.BASSLER,F.M.HUGHSON JRNL TITL SALMONELLA TYPHIMURIUM RECOGNIZES A CHEMICALLY DISTINCT FORM JRNL TITL 2 OF THE BACTERIAL QUORUM-SENSING SIGNAL AI-2 JRNL REF MOL.CELL V. 15 677 2004 JRNL REFN ISSN 1097-2765 JRNL PMID 15350213 JRNL DOI 10.1016/J.MOLCEL.2004.07.020 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.13 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) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 25812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2546 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 380 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2402 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 348 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 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 : 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 1TM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; NSLS REMARK 200 BEAMLINE : NULL; X25 REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200H; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.9789, 0.9793, 0.9500 REMARK 200 MONOCHROMATOR : YALE MIRRORS; SI111 REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV; ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 27.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, NACL, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 25K, 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 18.99200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.12200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.98950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.12200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.99200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.98950 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 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 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 25 REMARK 465 SER A 26 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 ASP A 116 -78.20 68.23 REMARK 500 LYS A 152 57.08 -103.86 REMARK 500 SER A 160 -73.76 -53.96 REMARK 500 ASN A 195 23.45 49.71 REMARK 500 TYR A 211 78.45 -119.37 REMARK 500 PRO A 220 48.22 -78.05 REMARK 500 ASN A 239 18.28 56.31 REMARK 500 LEU A 265 -138.96 -178.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TJY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SALMONELLA TYPHIMURIUM AI-2 RECEPTOR LSRB REMARK 900 IN COMPLEX WITH R-THMF REMARK 900 RELATED ID: 1JX6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE VIBRIO HARVEYI AI-2 RECEPTOR LUXP IN REMARK 900 COMPLEX WITH S-THMF-BORATE DBREF 1TM2 A 27 340 UNP Q8Z2X8 Q8Z2X8_SALTI 27 340 SEQADV 1TM2 GLY A 25 UNP Q8Z2X8 CLONING ARTIFACT SEQADV 1TM2 SER A 26 UNP Q8Z2X8 CLONING ARTIFACT SEQRES 1 A 316 GLY SER ALA GLU ARG ILE ALA PHE ILE PRO LYS LEU VAL SEQRES 2 A 316 GLY VAL GLY PHE PHE THR SER GLY GLY ASN GLY ALA GLN SEQRES 3 A 316 GLU ALA GLY LYS ALA LEU GLY ILE ASP VAL THR TYR ASP SEQRES 4 A 316 GLY PRO THR GLU PRO SER VAL SER GLY GLN VAL GLN LEU SEQRES 5 A 316 VAL ASN ASN PHE VAL ASN GLN GLY TYR ASP ALA ILE ILE SEQRES 6 A 316 VAL SER ALA VAL SER PRO ASP GLY LEU CYS PRO ALA LEU SEQRES 7 A 316 LYS ARG ALA MET GLN ARG GLY VAL LYS ILE LEU THR TRP SEQRES 8 A 316 ASP SER ASP THR LYS PRO GLU CYS ARG SER TYR TYR ILE SEQRES 9 A 316 ASN GLN GLY THR PRO LYS GLN LEU GLY SER MET LEU VAL SEQRES 10 A 316 GLU MET ALA ALA HIS GLN VAL ASP LYS GLU LYS ALA LYS SEQRES 11 A 316 VAL ALA PHE PHE TYR SER SER PRO THR VAL THR ASP GLN SEQRES 12 A 316 ASN GLN TRP VAL LYS GLU ALA LYS ALA LYS ILE SER GLN SEQRES 13 A 316 GLU HIS PRO GLY TRP GLU ILE VAL THR THR GLN PHE GLY SEQRES 14 A 316 TYR ASN ASP ALA THR LYS SER LEU GLN THR ALA GLU GLY SEQRES 15 A 316 ILE ILE LYS ALA TYR PRO ASP LEU ASP ALA ILE ILE ALA SEQRES 16 A 316 PRO ASP ALA ASN ALA LEU PRO ALA ALA ALA GLN ALA ALA SEQRES 17 A 316 GLU ASN LEU LYS ARG ASN ASN LEU ALA ILE VAL GLY PHE SEQRES 18 A 316 SER THR PRO ASN VAL MET ARG PRO TYR VAL GLN ARG GLY SEQRES 19 A 316 THR VAL LYS GLU PHE GLY LEU TRP ASP VAL VAL GLN GLN SEQRES 20 A 316 GLY LYS ILE SER VAL TYR VAL ALA ASN ALA LEU LEU LYS SEQRES 21 A 316 ASN MET PRO MET ASN VAL GLY ASP SER LEU ASP ILE PRO SEQRES 22 A 316 GLY ILE GLY LYS VAL THR VAL SER PRO ASN SER GLU GLN SEQRES 23 A 316 GLY TYR HIS TYR GLU ALA LYS GLY ASN GLY ILE VAL LEU SEQRES 24 A 316 LEU PRO GLU ARG VAL ILE PHE ASN LYS ASP ASN ILE ASP SEQRES 25 A 316 LYS TYR ASP PHE FORMUL 2 HOH *348(H2 O) HELIX 1 1 VAL A 39 GLY A 57 1 19 HELIX 2 2 SER A 69 GLN A 83 1 15 HELIX 3 3 LEU A 98 ARG A 108 1 11 HELIX 4 4 LYS A 120 ARG A 124 5 5 HELIX 5 5 THR A 132 VAL A 148 1 17 HELIX 6 6 VAL A 164 HIS A 182 1 19 HELIX 7 7 ASP A 196 TYR A 211 1 16 HELIX 8 8 ASN A 223 LEU A 235 1 13 HELIX 9 9 THR A 247 ARG A 257 1 11 HELIX 10 10 ASP A 267 LYS A 284 1 18 HELIX 11 11 PRO A 306 GLY A 311 5 6 HELIX 12 12 ASN A 334 TYR A 338 5 5 SHEET 1 A 8 ASP A 59 TYR A 62 0 SHEET 2 A 8 ARG A 29 ILE A 33 1 N ILE A 30 O THR A 61 SHEET 3 A 8 ALA A 87 VAL A 90 1 O ILE A 89 N ILE A 33 SHEET 4 A 8 LYS A 111 TRP A 115 1 O LYS A 111 N ILE A 88 SHEET 5 A 8 TYR A 126 ASN A 129 1 O ILE A 128 N THR A 114 SHEET 6 A 8 GLY A 320 LEU A 323 1 O VAL A 322 N TYR A 127 SHEET 7 A 8 GLY A 300 SER A 305 -1 N SER A 305 O ILE A 321 SHEET 8 A 8 SER A 293 ILE A 296 -1 N ILE A 296 O GLY A 300 SHEET 1 B 4 GLU A 186 PHE A 192 0 SHEET 2 B 4 LYS A 154 TYR A 159 1 N VAL A 155 O GLU A 186 SHEET 3 B 4 ALA A 216 ALA A 219 1 O ILE A 218 N ALA A 156 SHEET 4 B 4 ALA A 241 GLY A 244 1 O VAL A 243 N ALA A 219 SHEET 1 C 2 PHE A 263 LEU A 265 0 SHEET 2 C 2 VAL A 328 PHE A 330 -1 O PHE A 330 N PHE A 263 SSBOND 1 CYS A 99 CYS A 123 1555 1555 2.03 CRYST1 37.984 73.979 116.244 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 0.026327 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013517 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008603 0.00000