PDB Short entry for 4DOM HEADER SIGNALING PROTEIN 09-FEB-12 4DOM TITLE CRYSTAL STRUCTURE OF THE TIR-DOMAIN OF HUMAN MYELOID DIFFERENTIATION TITLE 2 PRIMARY RESPONSE PROTEIN (MYD88) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD88; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TIR DOMAIN, UNP RESIDUES 157-296; COMPND 5 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: MYD88; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS MYD88_HUMAN, TIR-DOMAIN, TOLL-LIKE RECEPTOR, ADOPTER DOMAIN, INNATE KEYWDS 2 IMMUNE SIGNALING, TIRAP/MAL, SIGNALING PROTEIN, LYSINE METHYLATION EXPDTA X-RAY DIFFRACTION AUTHOR J.S.JIANG,G.A.SNYDER,T.XIAO REVDAT 6 06-DEC-23 4DOM 1 REMARK REVDAT 5 13-SEP-23 4DOM 1 REMARK SEQADV REVDAT 4 17-JUL-19 4DOM 1 REMARK LINK REVDAT 3 08-MAY-13 4DOM 1 JRNL REVDAT 2 24-APR-13 4DOM 1 JRNL REVDAT 1 10-APR-13 4DOM 0 JRNL AUTH G.A.SNYDER,C.CIRL,J.JIANG,K.CHEN,A.WALDHUBER,P.SMITH, JRNL AUTH 2 F.ROMMLER,N.SNYDER,T.FRESQUEZ,S.DURR,N.TJANDRA,T.MIETHKE, JRNL AUTH 3 T.S.XIAO JRNL TITL MOLECULAR MECHANISMS FOR THE SUBVERSION OF MYD88 SIGNALING JRNL TITL 2 BY TCPC FROM VIRULENT UROPATHOGENIC ESCHERICHIA COLI. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 6985 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23569230 JRNL DOI 10.1073/PNAS.1215770110 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 10821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 560 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 42.5209 - 2.8545 0.96 2775 169 0.1775 0.2017 REMARK 3 2 2.8545 - 2.2657 0.98 2728 149 0.1767 0.2313 REMARK 3 3 2.2657 - 1.9793 0.94 2618 124 0.1716 0.2335 REMARK 3 4 1.9793 - 1.7980 0.78 2140 118 0.2138 0.2562 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.49 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 71.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.67990 REMARK 3 B22 (A**2) : -1.21920 REMARK 3 B33 (A**2) : 7.89910 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1198 REMARK 3 ANGLE : 1.107 1618 REMARK 3 CHIRALITY : 0.092 177 REMARK 3 PLANARITY : 0.007 201 REMARK 3 DIHEDRAL : 16.828 459 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 4DOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI MIRROR 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 : 11360 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.798 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.46700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2JS7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 0.1M IMMIDAZOLE PH 8.0, REMARK 280 0.2M NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 16.70750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.24750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.99550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.24750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.70750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.99550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASP A 156 CG OD1 OD2 REMARK 480 VAL A 204 CG1 REMARK 480 PRO A 245 CB CG REMARK 480 LYS A 262 CD CE NZ REMARK 480 ILE A 267 CD1 REMARK 480 PHE A 270 CG CD1 CD2 CE1 CE2 CZ REMARK 480 THR A 281 N REMARK 480 LYS A 282 CG CD CE NZ REMARK 480 TRP A 284 CD2 CE3 CZ2 CZ3 CH2 DBREF 4DOM A 157 296 UNP Q99836 MYD88_HUMAN 157 296 SEQADV 4DOM ASP A 156 UNP Q99836 EXPRESSION TAG SEQRES 1 A 141 ASP MET PRO GLU ARG PHE ASP ALA PHE ILE CSO TYR CYS SEQRES 2 A 141 PRO SER ASP ILE GLN PHE VAL GLN GLU MET ILE ARG GLN SEQRES 3 A 141 LEU GLU GLN THR ASN TYR ARG LEU MLY LEU CYS VAL SER SEQRES 4 A 141 ASP ARG ASP VAL LEU PRO GLY THR CYS VAL TRP SER ILE SEQRES 5 A 141 ALA SER GLU LEU ILE GLU MLY ARG CYS ARG ARG MET VAL SEQRES 6 A 141 VAL VAL VAL SER ASP ASP TYR LEU GLN SER LYS GLU CSO SEQRES 7 A 141 ASP PHE GLN THR MLY PHE ALA LEU SER LEU SER PRO GLY SEQRES 8 A 141 ALA HIS GLN LYS ARG LEU ILE PRO ILE MLY TYR MLY ALA SEQRES 9 A 141 MET LYS LYS GLU PHE PRO SER ILE LEU ARG PHE ILE THR SEQRES 10 A 141 VAL CYS ASP TYR THR ASN PRO CYS THR LYS SER TRP PHE SEQRES 11 A 141 TRP THR ARG LEU ALA LYS ALA LEU SER LEU PRO MODRES 4DOM CSO A 166 CYS S-HYDROXYCYSTEINE MODRES 4DOM MLY A 190 LYS N-DIMETHYL-LYSINE MODRES 4DOM MLY A 214 LYS N-DIMETHYL-LYSINE MODRES 4DOM CSO A 233 CYS S-HYDROXYCYSTEINE MODRES 4DOM MLY A 238 LYS N-DIMETHYL-LYSINE MODRES 4DOM MLY A 256 LYS N-DIMETHYL-LYSINE MODRES 4DOM MLY A 258 LYS N-DIMETHYL-LYSINE HET CSO A 166 7 HET MLY A 190 11 HET MLY A 214 11 HET CSO A 233 7 HET MLY A 238 11 HET MLY A 256 11 HET MLY A 258 11 HETNAM CSO S-HYDROXYCYSTEINE HETNAM MLY N-DIMETHYL-LYSINE FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 1 MLY 5(C8 H18 N2 O2) FORMUL 2 HOH *102(H2 O) HELIX 1 1 CYS A 168 SER A 170 5 3 HELIX 2 2 ASP A 171 GLN A 184 1 14 HELIX 3 3 ASP A 195 LEU A 199 5 5 HELIX 4 4 ALA A 208 GLU A 210 5 3 HELIX 5 5 LEU A 211 ARG A 215 1 5 HELIX 6 6 SER A 224 GLN A 229 1 6 HELIX 7 7 SER A 230 LEU A 243 1 14 HELIX 8 8 ALA A 247 ARG A 251 1 5 HELIX 9 9 PRO A 265 ARG A 269 5 5 HELIX 10 10 ASN A 278 LYS A 282 5 5 HELIX 11 11 TRP A 284 LEU A 295 1 12 SHEET 1 A 6 TRP A 205 SER A 206 0 SHEET 2 A 6 LEU A 191 VAL A 193 1 N VAL A 193 O TRP A 205 SHEET 3 A 6 PHE A 161 CSO A 166 1 N ILE A 165 O CYS A 192 SHEET 4 A 6 CYS A 216 VAL A 223 1 O VAL A 220 N CSO A 166 SHEET 5 A 6 LEU A 252 MLY A 256 1 O ILE A 255 N VAL A 221 SHEET 6 A 6 CYS A 274 ASP A 275 1 O CYS A 274 N PRO A 254 SSBOND 1 CYS A 203 CYS A 280 1555 1455 2.03 LINK C ILE A 165 N CSO A 166 1555 1555 1.33 LINK C CSO A 166 N TYR A 167 1555 1555 1.33 LINK C LEU A 189 N MLY A 190 1555 1555 1.33 LINK C MLY A 190 N LEU A 191 1555 1555 1.33 LINK C GLU A 213 N MLY A 214 1555 1555 1.33 LINK C MLY A 214 N ARG A 215 1555 1555 1.33 LINK C GLU A 232 N CSO A 233 1555 1555 1.33 LINK C CSO A 233 N ASP A 234 1555 1555 1.33 LINK C THR A 237 N MLY A 238 1555 1555 1.33 LINK C MLY A 238 N PHE A 239 1555 1555 1.33 LINK C ILE A 255 N MLY A 256 1555 1555 1.33 LINK C MLY A 256 N TYR A 257 1555 1555 1.32 LINK C TYR A 257 N MLY A 258 1555 1555 1.33 LINK C MLY A 258 N ALA A 259 1555 1555 1.33 CRYST1 33.415 57.991 62.495 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 0.029927 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016001 0.00000