PDB Short entry for 4LQD HEADER IMMUNE SYSTEM 17-JUL-13 4LQD TITLE THE CRYSTAL STRUCTURES OF THE BRUCELLA PROTEIN TCPB AND THE TLR TITLE 2 ADAPTOR PROTEIN TIRAP SHOW STRUCTURAL DIFFERENCES IN MICROBIAL TIR TITLE 3 MIMICRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL/INTERLEUKIN-1 RECEPTOR DOMAIN-CONTAINING ADAPTER COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: TIRAP TIR DOMAIN (UNP RESIDUES 81-221); COMPND 6 SYNONYM: TIR DOMAIN-CONTAINING ADAPTER PROTEIN, ADAPTOR PROTEIN COMPND 7 WYATT, MYD88 ADAPTER-LIKE PROTEIN, MYD88-2; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TIRAP, MAL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FLAVODOXIN FOLD, TOLL-LIKE RECEPTOR SIGNALING ADAPTOR, MYD88, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR G.A.SNYDER,P.SMITH,J.JIANG,T.S.XIAO REVDAT 2 09-APR-14 4LQD 1 JRNL REVDAT 1 04-DEC-13 4LQD 0 JRNL AUTH G.A.SNYDER,D.DEREDGE,A.WALDHUBER,T.FRESQUEZ,D.Z.WILKINS, JRNL AUTH 2 P.T.SMITH,S.DURR,C.CIRL,J.JIANG,W.JENNINGS,T.LUCHETTI, JRNL AUTH 3 N.SNYDER,E.J.SUNDBERG,P.WINTRODE,T.MIETHKE,T.S.XIAO JRNL TITL CRYSTAL STRUCTURES OF THE TOLL/INTERLEUKIN-1 RECEPTOR (TIR) JRNL TITL 2 DOMAINS FROM THE BRUCELLA PROTEIN TCPB AND HOST ADAPTOR JRNL TITL 3 TIRAP REVEAL MECHANISMS OF MOLECULAR MIMICRY. JRNL REF J.BIOL.CHEM. V. 289 669 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24275656 JRNL DOI 10.1074/JBC.M113.523407 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 572 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 39.1675 - 3.8890 1.00 2998 142 0.1829 0.1796 REMARK 3 2 3.8890 - 3.0872 1.00 2839 148 0.2038 0.2405 REMARK 3 3 3.0872 - 2.6971 1.00 2803 141 0.2467 0.2357 REMARK 3 4 2.6971 - 2.4505 1.00 2786 141 0.2687 0.2954 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.540 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 : 0.006 1012 REMARK 3 ANGLE : 0.978 1366 REMARK 3 CHIRALITY : 0.034 148 REMARK 3 PLANARITY : 0.007 175 REMARK 3 DIHEDRAL : 13.426 375 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 4LQD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-13. REMARK 100 THE RCSB ID CODE IS RCSB080953. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12002 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 10.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5%MPD,100MM CHES PH 9.0, 100MM NACL REMARK 280 AND 24% GLYCEROL CRYO, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.32500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.78500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.78500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.48750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.78500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.78500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.16250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.78500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.78500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.48750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.78500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.78500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.16250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.32500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 110 REMARK 465 THR A 111 REMARK 465 ALA A 112 REMARK 465 SER A 113 REMARK 465 LEU A 114 REMARK 465 ARG A 115 REMARK 465 CYS A 116 REMARK 465 PHE A 117 REMARK 465 LEU A 118 REMARK 465 GLN A 119 REMARK 465 LEU A 120 REMARK 465 ARG A 121 REMARK 465 ASP A 122 REMARK 465 ALA A 123 REMARK 465 THR A 124 REMARK 465 ALA A 168 REMARK 465 PRO A 169 REMARK 465 GLY A 170 REMARK 465 ALA A 171 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 208 N C O REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LQC RELATED DB: PDB DBREF 4LQD A 81 221 UNP P58753 TIRAP_HUMAN 81 221 SEQADV 4LQD GLY A 78 UNP P58753 EXPRESSION TAG SEQADV 4LQD VAL A 79 UNP P58753 EXPRESSION TAG SEQADV 4LQD ASP A 80 UNP P58753 EXPRESSION TAG SEQRES 1 A 144 GLY VAL ASP ARG TRP SER LYS ASP TYR ASP VAL CYS VAL SEQRES 2 A 144 CME HIS SER GLU GLU ASP LEU VAL ALA ALA GLN ASP LEU SEQRES 3 A 144 VAL SER TYR LEU GLU GLY SER THR ALA SER LEU ARG CYS SEQRES 4 A 144 PHE LEU GLN LEU ARG ASP ALA THR PRO GLY GLY ALA ILE SEQRES 5 A 144 VAL SER GLU LEU CYS GLN ALA LEU SER SER SER HIS CYS SEQRES 6 A 144 ARG VAL LEU LEU ILE THR PRO GLY PHE LEU GLN ASP PRO SEQRES 7 A 144 TRP CME LYS TYR GLN MET LEU GLN ALA LEU THR GLU ALA SEQRES 8 A 144 PRO GLY ALA GLU GLY CYS THR ILE PRO LEU LEU SER GLY SEQRES 9 A 144 LEU SER ARG ALA ALA TYR PRO PRO GLU LEU ARG PHE MET SEQRES 10 A 144 TYR TYR VAL ASP GLY ARG GLY PRO ASP GLY GLY PHE ARG SEQRES 11 A 144 GLN VAL LYS GLU ALA VAL MET ARG TYR LEU GLN THR LEU SEQRES 12 A 144 SER MODRES 4LQD CME A 91 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 4LQD CME A 157 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME A 91 10 HET CME A 157 10 HET GOL A 301 6 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *59(H2 O) HELIX 1 1 ASP A 80 LYS A 84 5 5 HELIX 2 2 SER A 93 GLU A 95 5 3 HELIX 3 3 ASP A 96 GLY A 109 1 14 HELIX 4 4 THR A 148 ASP A 154 1 7 HELIX 5 5 ASP A 154 LEU A 165 1 12 HELIX 6 6 SER A 183 TYR A 187 5 5 HELIX 7 7 PRO A 188 MET A 194 5 7 HELIX 8 8 GLY A 201 GLY A 204 5 4 HELIX 9 9 GLY A 205 THR A 219 1 15 SHEET 1 A 5 SER A 131 LEU A 133 0 SHEET 2 A 5 TYR A 86 CME A 91 1 N VAL A 90 O GLU A 132 SHEET 3 A 5 SER A 140 ILE A 147 1 O VAL A 144 N CME A 91 SHEET 4 A 5 THR A 175 LEU A 179 1 O LEU A 178 N LEU A 145 SHEET 5 A 5 VAL A 197 ASP A 198 1 O VAL A 197 N PRO A 177 SSBOND 1 CYS A 89 CYS A 134 1555 1555 2.05 SSBOND 2 CYS A 142 CYS A 174 1555 1555 2.05 LINK C VAL A 90 N CME A 91 1555 1555 1.33 LINK C CME A 91 N HIS A 92 1555 1555 1.33 LINK C TRP A 156 N CME A 157 1555 1555 1.33 LINK C CME A 157 N LYS A 158 1555 1555 1.33 SITE 1 AC1 4 ARG A 81 TRP A 82 ARG A 192 SER A 221 CRYST1 87.570 87.570 80.650 90.00 90.00 90.00 P 43 21 2 8 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 0.011419 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012399 0.00000