HEADER SIGNALING PROTEIN 24-JUL-18 6AC0 TITLE CRYSTAL STRUCTURE OF TRADD DEATH DOMAIN GLCNACYLATED BY EPEC EFFECTOR TITLE 2 NLEB COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR TYPE 1-ASSOCIATED DEATH COMPND 3 DOMAIN PROTEIN; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TNFR1-ASSOCIATED DEATH DOMAIN PROTEIN,TNFRSF1A-ASSOCIATED COMPND 6 VIA DEATH DOMAIN; COMPND 7 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: TRADD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX6P KEYWDS APOPTOSIS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.DING,F.SHAO REVDAT 4 22-NOV-23 6AC0 1 HETSYN REVDAT 3 29-JUL-20 6AC0 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 26-JUN-19 6AC0 1 JRNL REVDAT 1 01-MAY-19 6AC0 0 JRNL AUTH J.DING,X.PAN,L.DU,Q.YAO,J.XUE,H.YAO,D.C.WANG,S.LI,F.SHAO JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO HOST DEATH DOMAINS JRNL TITL 2 INACTIVATION BY THE BACTERIAL ARGININE GLCNACYLTRANSFERASE JRNL TITL 3 EFFECTOR. JRNL REF MOL.CELL V. 74 922 2019 JRNL REFN ISSN 1097-2765 JRNL PMID 30979585 JRNL DOI 10.1016/J.MOLCEL.2019.03.028 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 20047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1022 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 28.4400 - 2.7711 0.85 2683 125 0.1982 0.2216 REMARK 3 2 2.7711 - 2.1998 0.93 2677 141 0.1870 0.2009 REMARK 3 3 2.1998 - 1.9218 0.96 2727 162 0.1657 0.2329 REMARK 3 4 1.9218 - 1.7461 0.98 2762 143 0.1733 0.2522 REMARK 3 5 1.7461 - 1.6210 0.99 2732 155 0.1692 0.2271 REMARK 3 6 1.6210 - 1.5254 0.99 2750 144 0.1648 0.2186 REMARK 3 7 1.5254 - 1.4490 0.99 2694 152 0.2035 0.2693 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.740 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 : 0.006 958 REMARK 3 ANGLE : 0.873 1296 REMARK 3 CHIRALITY : 0.066 143 REMARK 3 PLANARITY : 0.004 174 REMARK 3 DIHEDRAL : 20.633 374 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 6AC0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008468. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97899 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20061 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.449 REMARK 200 RESOLUTION RANGE LOW (A) : 28.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.34900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3OQ9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M NA/KPO4, PH 6.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 132.36000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 14.30000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 14.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.18000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 14.30000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 14.30000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 198.54000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 14.30000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.30000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.18000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 14.30000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.30000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 198.54000 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 132.36000 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 PRO A 195 REMARK 465 PRO A 196 REMARK 465 PRO A 197 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 NH2 ARG A 231 O HOH A 501 2.14 REMARK 500 OG SER A 225 O HOH A 502 2.16 REMARK 500 OG1 THR A 305 O HOH A 503 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6AC0 A 195 312 UNP Q15628 TRADD_HUMAN 195 312 SEQRES 1 A 118 PRO PRO PRO PRO ALA GLN THR PHE LEU PHE GLN GLY GLN SEQRES 2 A 118 PRO VAL VAL ASN ARG PRO LEU SER LEU LYS ASP GLN GLN SEQRES 3 A 118 THR PHE ALA ARG SER VAL GLY LEU LYS TRP ARG LYS VAL SEQRES 4 A 118 GLY ARG SER LEU GLN ARG GLY CYS ARG ALA LEU ARG ASP SEQRES 5 A 118 PRO ALA LEU ASP SER LEU ALA TYR GLU TYR GLU ARG GLU SEQRES 6 A 118 GLY LEU TYR GLU GLN ALA PHE GLN LEU LEU ARG ARG PHE SEQRES 7 A 118 VAL GLN ALA GLU GLY ARG ARG ALA THR LEU GLN ARG LEU SEQRES 8 A 118 VAL GLU ALA LEU GLU GLU ASN GLU LEU THR SER LEU ALA SEQRES 9 A 118 GLU ASP LEU LEU GLY LEU THR ASP PRO ASN GLY GLY LEU SEQRES 10 A 118 ALA HET NAG A 401 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 HOH *104(H2 O) HELIX 1 AA1 SER A 215 VAL A 226 1 12 HELIX 2 AA2 LYS A 229 ARG A 239 1 11 HELIX 3 AA3 GLY A 240 ARG A 245 5 6 HELIX 4 AA4 PRO A 247 GLU A 257 1 11 HELIX 5 AA5 GLY A 260 GLY A 277 1 18 HELIX 6 AA6 ARG A 278 ALA A 280 5 3 HELIX 7 AA7 THR A 281 ASN A 292 1 12 HELIX 8 AA8 LEU A 294 LEU A 302 1 9 SHEET 1 AA1 2 THR A 201 PHE A 204 0 SHEET 2 AA1 2 GLN A 207 VAL A 210 -1 O GLN A 207 N PHE A 204 LINK NH2 ARG A 235 C1 NAG A 401 1555 1555 1.44 CISPEP 1 ASP A 246 PRO A 247 0 6.13 CRYST1 28.600 28.600 264.720 90.00 90.00 90.00 P 41 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 0.034965 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003778 0.00000