HEADER SIGNALING PROTEIN 19-AUG-16 5GTA TITLE 3D CRYSTAL STRUCTURE OF LSRB BOUND TO FURANOSYL DIESTER (R)-THMF, FROM TITLE 2 SALMONELLA TYPHI COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOINDUCER 2-BINDING PROTEIN LSRB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AI-2-BINDING PROTEIN LSRB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHI; SOURCE 4 ORGANISM_TAXID: 90370; SOURCE 5 GENE: LSRB, STY3793, T3541; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30B(+) KEYWDS ABC TRANSPORTER, SALMONELLA TYPHI, AUTOINDUCER-2, LUXS REGULATED, TWO KEYWDS 2 COMPONENT SYSTEM, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.GOPINATH,P.PERUMAL,R.RAHUL,A.AROCKIASAMY,N.SUNDARABAALAJI REVDAT 3 08-NOV-23 5GTA 1 REMARK REVDAT 2 29-JUL-20 5GTA 1 COMPND REMARK HETNAM SITE REVDAT 2 2 1 ATOM REVDAT 1 23-AUG-17 5GTA 0 JRNL AUTH S.GOPINATH,P.PERUMAL,R.RAHUL,A.AROCKIASAMY,N.SUNDARABAALAJI JRNL TITL 3D CRYSTAL STRUCTURE OF LSRB BOUND TO FURANOSYL DIESTER JRNL TITL 2 (R)-THMF, FROM SALMONELLA TYPHI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 6329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 293 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.1369 - 3.7762 1.00 3094 161 0.1770 0.2216 REMARK 3 2 3.7762 - 2.9976 0.98 2942 132 0.2303 0.3222 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.460 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 2462 REMARK 3 ANGLE : 0.552 3349 REMARK 3 CHIRALITY : 0.020 373 REMARK 3 PLANARITY : 0.002 439 REMARK 3 DIHEDRAL : 10.711 899 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0-9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6389 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.998 REMARK 200 RESOLUTION RANGE LOW (A) : 57.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1TJY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K 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 20.79100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.87650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.87700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.87650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.79100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.87700 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ARG A 3 REMARK 465 HIS A 4 REMARK 465 SER A 5 REMARK 465 ILE A 6 REMARK 465 LYS A 7 REMARK 465 MET A 8 REMARK 465 ILE A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 THR A 13 REMARK 465 ALA A 14 REMARK 465 PHE A 15 REMARK 465 GLY A 16 REMARK 465 LEU A 17 REMARK 465 ALA A 18 REMARK 465 SER A 19 REMARK 465 ALA A 20 REMARK 465 VAL A 21 REMARK 465 MET A 22 REMARK 465 THR A 23 REMARK 465 VAL A 24 REMARK 465 GLN A 25 REMARK 465 ALA A 26 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 ARG A 104 CZ NH1 NH2 REMARK 470 LYS A 134 NZ 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 OD2 ASP A 333 O HOH A 501 1.98 REMARK 500 O LYS A 261 O HOH A 502 2.07 REMARK 500 NE2 GLN A 167 O4 PAV A 401 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 PRO A 68 95.07 -69.31 REMARK 500 ASP A 116 -75.96 58.11 REMARK 500 THR A 119 -152.95 -96.23 REMARK 500 PHE A 158 101.47 -160.99 REMARK 500 TYR A 159 -158.15 -134.77 REMARK 500 SER A 160 -75.08 -71.95 REMARK 500 LEU A 265 -142.67 -163.45 REMARK 500 HIS A 313 67.28 -107.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TJY RELATED DB: PDB REMARK 900 THIS ENTRY IS A HOMOLOGOUS PROTEIN FROM S.TYPHIMURIUM DBREF 5GTA A 1 340 UNP Q8Z2X8 LSRB_SALTI 1 340 SEQRES 1 A 340 MET ALA ARG HIS SER ILE LYS MET ILE ALA LEU LEU THR SEQRES 2 A 340 ALA PHE GLY LEU ALA SER ALA VAL MET THR VAL GLN ALA SEQRES 3 A 340 ALA GLU ARG ILE ALA PHE ILE PRO LYS LEU VAL GLY VAL SEQRES 4 A 340 GLY PHE PHE THR SER GLY GLY ASN GLY ALA GLN GLU ALA SEQRES 5 A 340 GLY LYS ALA LEU GLY ILE ASP VAL THR TYR ASP GLY PRO SEQRES 6 A 340 THR GLU PRO SER VAL SER GLY GLN VAL GLN LEU VAL ASN SEQRES 7 A 340 ASN PHE VAL ASN GLN GLY TYR ASP ALA ILE ILE VAL SER SEQRES 8 A 340 ALA VAL SER PRO ASP GLY LEU CYS PRO ALA LEU LYS ARG SEQRES 9 A 340 ALA MET GLN ARG GLY VAL LYS ILE LEU THR TRP ASP SER SEQRES 10 A 340 ASP THR LYS PRO GLU CYS ARG SER TYR TYR ILE ASN GLN SEQRES 11 A 340 GLY THR PRO LYS GLN LEU GLY SER MET LEU VAL GLU MET SEQRES 12 A 340 ALA ALA HIS GLN VAL ASP LYS GLU LYS ALA LYS VAL ALA SEQRES 13 A 340 PHE PHE TYR SER SER PRO THR VAL THR ASP GLN ASN GLN SEQRES 14 A 340 TRP VAL LYS GLU ALA LYS ALA LYS ILE SER GLN GLU HIS SEQRES 15 A 340 PRO GLY TRP GLU ILE VAL THR THR GLN PHE GLY TYR ASN SEQRES 16 A 340 ASP ALA THR LYS SER LEU GLN THR ALA GLU GLY ILE ILE SEQRES 17 A 340 LYS ALA TYR PRO ASP LEU ASP ALA ILE ILE ALA PRO ASP SEQRES 18 A 340 ALA ASN ALA LEU PRO ALA ALA ALA GLN ALA ALA GLU ASN SEQRES 19 A 340 LEU LYS ARG ASN ASN LEU ALA ILE VAL GLY PHE SER THR SEQRES 20 A 340 PRO ASN VAL MET ARG PRO TYR VAL GLN ARG GLY THR VAL SEQRES 21 A 340 LYS GLU PHE GLY LEU TRP ASP VAL VAL GLN GLN GLY LYS SEQRES 22 A 340 ILE SER VAL TYR VAL ALA ASN ALA LEU LEU LYS ASN MET SEQRES 23 A 340 PRO MET ASN VAL GLY ASP SER LEU ASP ILE PRO GLY ILE SEQRES 24 A 340 GLY LYS VAL THR VAL SER PRO ASN SER GLU GLN GLY TYR SEQRES 25 A 340 HIS TYR GLU ALA LYS GLY ASN GLY ILE VAL LEU LEU PRO SEQRES 26 A 340 GLU ARG VAL ILE PHE ASN LYS ASP ASN ILE ASP LYS TYR SEQRES 27 A 340 ASP PHE HET PAV A 401 10 HETNAM PAV (2R,4S)-2-METHYL-2,3,3,4-TETRAHYDROXYTETRAHYDROFURAN FORMUL 2 PAV C5 H10 O5 FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 VAL A 39 LEU A 56 1 18 HELIX 2 AA2 SER A 69 GLN A 83 1 15 HELIX 3 AA3 LEU A 98 GLN A 107 1 10 HELIX 4 AA4 THR A 132 ASP A 149 1 18 HELIX 5 AA5 VAL A 164 HIS A 182 1 19 HELIX 6 AA6 ASP A 196 TYR A 211 1 16 HELIX 7 AA7 ASN A 223 LEU A 235 1 13 HELIX 8 AA8 THR A 247 ARG A 257 1 11 HELIX 9 AA9 ASP A 267 LYS A 284 1 18 HELIX 10 AB1 PRO A 306 GLN A 310 5 5 SHEET 1 AA1 8 ASP A 59 TYR A 62 0 SHEET 2 AA1 8 ARG A 29 ILE A 33 1 N PHE A 32 O THR A 61 SHEET 3 AA1 8 ALA A 87 VAL A 90 1 O ILE A 89 N ALA A 31 SHEET 4 AA1 8 LYS A 111 TRP A 115 1 O LYS A 111 N ILE A 88 SHEET 5 AA1 8 TYR A 126 ASN A 129 1 O ILE A 128 N THR A 114 SHEET 6 AA1 8 GLY A 320 LEU A 323 1 O GLY A 320 N TYR A 127 SHEET 7 AA1 8 GLY A 300 SER A 305 -1 N SER A 305 O ILE A 321 SHEET 8 AA1 8 SER A 293 ILE A 296 -1 N ILE A 296 O GLY A 300 SHEET 1 AA2 4 TRP A 185 PHE A 192 0 SHEET 2 AA2 4 ALA A 153 TYR A 159 1 N ALA A 153 O GLU A 186 SHEET 3 AA2 4 ALA A 216 ALA A 219 1 O ILE A 218 N ALA A 156 SHEET 4 AA2 4 ALA A 241 GLY A 244 1 O VAL A 243 N ALA A 219 SHEET 1 AA3 2 PHE A 263 TRP A 266 0 SHEET 2 AA3 2 ARG A 327 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 41.582 61.754 115.753 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 0.024049 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016193 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008639 0.00000