HEADER SIGNALING PROTEIN 26-SEP-18 6MKZ TITLE CRYSTAL STRUCTURE OF MURINE 4-1BB/4-1BBL COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RESIDUES 139-309; COMPND 5 SYNONYM: 4-1BB LIGAND,4-1BBL; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 9; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: RESIDUES 24-160; COMPND 11 SYNONYM: 4-1BB LIGAND RECEPTOR,T-CELL ANTIGEN 4-1BB; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TNFSF9, CD137L, CD157L, LY63L; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PACGP67A; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 14 ORGANISM_COMMON: MOUSE; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 GENE: TNFRSF9, CD137, ILA, LY63; SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 18 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 22 EXPRESSION_SYSTEM_VECTOR: PACGP67A KEYWDS TNF, TNFR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.BITRA,D.M.ZAJONC,T.DOUKOV REVDAT 5 11-OCT-23 6MKZ 1 HETSYN REVDAT 4 29-JUL-20 6MKZ 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 20-FEB-19 6MKZ 1 JRNL REVDAT 2 26-DEC-18 6MKZ 1 JRNL REVDAT 1 19-DEC-18 6MKZ 0 JRNL AUTH A.BITRA,T.DOUKOV,G.DESTITO,M.CROFT,D.M.ZAJONC JRNL TITL CRYSTAL STRUCTURE OF THE M4-1BB/4-1BBL COMPLEX REVEALS AN JRNL TITL 2 UNUSUAL DIMERIC LIGAND THAT UNDERGOES STRUCTURAL CHANGES JRNL TITL 3 UPON 4-1BB RECEPTOR BINDING. JRNL REF J. BIOL. CHEM. V. 294 1831 2019 JRNL REFN ESSN 1083-351X JRNL PMID 30545939 JRNL DOI 10.1074/JBC.RA118.006297 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 25124 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1239 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 : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.57 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 503 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2501 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 479 REMARK 3 BIN R VALUE (WORKING SET) : 0.2462 REMARK 3 BIN FREE R VALUE : 0.3208 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.77 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 24 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3926 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 76.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.22890 REMARK 3 B22 (A**2) : 5.74750 REMARK 3 B33 (A**2) : -6.97640 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.350 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.417 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.261 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.384 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.258 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4124 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5638 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1822 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 696 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4124 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 557 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4421 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.24 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.59 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.85 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { C|145 - C|306 C|500 - C|502 } REMARK 3 ORIGIN FOR THE GROUP (A): 8.5164 9.1542 23.2319 REMARK 3 T TENSOR REMARK 3 T11: -0.2645 T22: 0.0198 REMARK 3 T33: -0.2311 T12: 0.0598 REMARK 3 T13: 0.0767 T23: 0.2654 REMARK 3 L TENSOR REMARK 3 L11: 5.4541 L22: 2.0636 REMARK 3 L33: 4.1569 L12: -0.6562 REMARK 3 L13: 1.2720 L23: -1.2929 REMARK 3 S TENSOR REMARK 3 S11: -0.1970 S12: -0.9927 S13: -0.8808 REMARK 3 S21: 0.2277 S22: 0.2680 S23: 0.0899 REMARK 3 S31: 0.3339 S32: -0.5031 S33: -0.0710 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|144 - A|308 A|500 - A|502 } REMARK 3 ORIGIN FOR THE GROUP (A): 14.7901 23.7573 38.9345 REMARK 3 T TENSOR REMARK 3 T11: -0.1042 T22: -0.1312 REMARK 3 T33: -0.2618 T12: 0.1192 REMARK 3 T13: -0.0291 T23: 0.0775 REMARK 3 L TENSOR REMARK 3 L11: 8.5164 L22: 4.5686 REMARK 3 L33: 4.9733 L12: -3.0157 REMARK 3 L13: -1.7547 L23: 0.7787 REMARK 3 S TENSOR REMARK 3 S11: 0.3318 S12: -0.4599 S13: 1.0872 REMARK 3 S21: 0.2259 S22: -0.1568 S23: -0.7298 REMARK 3 S31: -0.7061 S32: 0.1037 S33: -0.1750 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|22 - B|155 } REMARK 3 ORIGIN FOR THE GROUP (A): 0.4953 28.1840 7.7093 REMARK 3 T TENSOR REMARK 3 T11: -0.1844 T22: 0.1886 REMARK 3 T33: -0.0630 T12: 0.0572 REMARK 3 T13: -0.0423 T23: -0.1096 REMARK 3 L TENSOR REMARK 3 L11: 6.1382 L22: 0.1888 REMARK 3 L33: 0.0000 L12: -0.3384 REMARK 3 L13: 0.0803 L23: 0.2855 REMARK 3 S TENSOR REMARK 3 S11: -0.2181 S12: -0.7041 S13: 0.6629 REMARK 3 S21: -0.0745 S22: 0.0236 S23: 0.0143 REMARK 3 S31: -0.0694 S32: -0.0725 S33: 0.1945 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|28 - D|112 } REMARK 3 ORIGIN FOR THE GROUP (A): 5.6000 12.0235 55.8389 REMARK 3 T TENSOR REMARK 3 T11: 0.0987 T22: 0.3542 REMARK 3 T33: -0.5802 T12: 0.2190 REMARK 3 T13: 0.0427 T23: 0.2430 REMARK 3 L TENSOR REMARK 3 L11: 5.5144 L22: 4.9518 REMARK 3 L33: 2.9398 L12: -1.8235 REMARK 3 L13: -3.4205 L23: 0.4045 REMARK 3 S TENSOR REMARK 3 S11: 0.0598 S12: -0.7653 S13: -0.5033 REMARK 3 S21: 0.6508 S22: -0.3982 S23: 0.0163 REMARK 3 S31: 0.1872 S32: -0.0827 S33: 0.3384 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MKZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000237135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25447 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.624 REMARK 200 RESOLUTION RANGE LOW (A) : 76.859 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 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 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5WI8, 6MKB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.2M AMMONIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 30.74950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.57900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.23900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.57900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.74950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.23900 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 ASN A 139 REMARK 465 THR A 140 REMARK 465 THR A 141 REMARK 465 GLN A 142 REMARK 465 GLN A 143 REMARK 465 LEU A 237 REMARK 465 GLU A 309 REMARK 465 THR B 137 REMARK 465 ASN B 138 REMARK 465 CYS B 139 REMARK 465 SER B 140 REMARK 465 LEU B 141 REMARK 465 ASP B 142 REMARK 465 GLY B 143 REMARK 465 ARG B 144 REMARK 465 SER B 145 REMARK 465 VAL B 146 REMARK 465 LEU B 147 REMARK 465 LYS B 148 REMARK 465 THR B 149 REMARK 465 GLY B 150 REMARK 465 VAL B 156 REMARK 465 VAL B 157 REMARK 465 CYS B 158 REMARK 465 GLY B 159 REMARK 465 PRO B 160 REMARK 465 ASN C 139 REMARK 465 THR C 140 REMARK 465 THR C 141 REMARK 465 GLN C 142 REMARK 465 GLN C 143 REMARK 465 GLY C 144 REMARK 465 ASN C 212 REMARK 465 THR C 213 REMARK 465 GLY C 214 REMARK 465 PRO C 307 REMARK 465 TRP C 308 REMARK 465 GLU C 309 REMARK 465 ASP D 22 REMARK 465 PRO D 23 REMARK 465 VAL D 24 REMARK 465 GLN D 25 REMARK 465 ASN D 26 REMARK 465 SER D 27 REMARK 465 LYS D 113 REMARK 465 GLN D 114 REMARK 465 GLY D 115 REMARK 465 CYS D 116 REMARK 465 LYS D 117 REMARK 465 THR D 118 REMARK 465 CYS D 119 REMARK 465 SER D 120 REMARK 465 LEU D 121 REMARK 465 GLY D 122 REMARK 465 THR D 123 REMARK 465 PHE D 124 REMARK 465 ASN D 125 REMARK 465 ASP D 126 REMARK 465 GLN D 127 REMARK 465 ASN D 128 REMARK 465 GLY D 129 REMARK 465 THR D 130 REMARK 465 GLY D 131 REMARK 465 VAL D 132 REMARK 465 CYS D 133 REMARK 465 ARG D 134 REMARK 465 PRO D 135 REMARK 465 TRP D 136 REMARK 465 THR D 137 REMARK 465 ASN D 138 REMARK 465 CYS D 139 REMARK 465 SER D 140 REMARK 465 LEU D 141 REMARK 465 ASP D 142 REMARK 465 GLY D 143 REMARK 465 ARG D 144 REMARK 465 SER D 145 REMARK 465 VAL D 146 REMARK 465 LEU D 147 REMARK 465 LYS D 148 REMARK 465 THR D 149 REMARK 465 GLY D 150 REMARK 465 THR D 151 REMARK 465 THR D 152 REMARK 465 GLU D 153 REMARK 465 LYS D 154 REMARK 465 ASP D 155 REMARK 465 VAL D 156 REMARK 465 VAL D 157 REMARK 465 CYS D 158 REMARK 465 GLY D 159 REMARK 465 PRO D 160 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 GLN A 179 CG CD OE1 NE2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 GLU A 189 CG CD OE1 OE2 REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 ASP A 233 CG OD1 OD2 REMARK 470 PHE A 234 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 MET A 248 CG SD CE REMARK 470 ASN A 250 CG OD1 ND2 REMARK 470 ARG A 268 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 281 CG CD OE1 NE2 REMARK 470 ARG A 285 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 LYS A 303 CG CD CE NZ REMARK 470 TRP A 308 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 308 CZ3 CH2 REMARK 470 TYR B 40 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN B 97 CG CD OE1 NE2 REMARK 470 ARG B 106 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 113 CG CD CE NZ REMARK 470 GLN B 114 CG CD OE1 NE2 REMARK 470 LYS B 117 CG CD CE NZ REMARK 470 LEU B 121 CG CD1 CD2 REMARK 470 TRP B 136 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 136 CZ3 CH2 REMARK 470 LYS B 154 CG CD CE NZ REMARK 470 ASP B 155 CG OD1 OD2 REMARK 470 GLN C 179 CG CD OE1 NE2 REMARK 470 HIS C 215 CG ND1 CD2 CE1 NE2 REMARK 470 LYS C 216 CG CD CE NZ REMARK 470 GLN C 218 CG CD OE1 NE2 REMARK 470 LYS C 228 CG CD CE NZ REMARK 470 GLU C 242 CG CD OE1 OE2 REMARK 470 GLU C 249 CG CD OE1 OE2 REMARK 470 LYS C 264 CG CD CE NZ REMARK 470 GLN C 281 CG CD OE1 NE2 REMARK 470 ASP C 282 CG OD1 OD2 REMARK 470 LYS C 303 CG CD CE NZ REMARK 470 LYS D 39 CG CD CE NZ REMARK 470 TYR D 40 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS D 45 CG CD CE NZ REMARK 470 LYS D 74 CG CD CE NZ REMARK 470 LYS D 75 CG CD CE NZ REMARK 470 HIS D 81 CG ND1 CD2 CE1 NE2 REMARK 470 GLU D 84 CG CD OE1 OE2 REMARK 470 GLU D 86 CG CD OE1 OE2 REMARK 470 ARG D 100 CG CD NE CZ NH1 NH2 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 ASN A 155 60.05 36.12 REMARK 500 ALA A 157 -61.31 -138.34 REMARK 500 ASN A 161 75.94 -112.95 REMARK 500 GLN A 230 151.73 67.60 REMARK 500 ASN A 293 94.07 -69.88 REMARK 500 ASN B 30 39.28 -97.34 REMARK 500 SER B 53 107.79 -163.24 REMARK 500 LYS B 74 -70.83 -105.93 REMARK 500 THR B 112 -167.25 -129.58 REMARK 500 SER B 120 -173.25 -55.63 REMARK 500 ASP C 232 -50.44 -26.51 REMARK 500 ASN C 236 38.88 -79.71 REMARK 500 ASN C 293 94.01 -69.64 REMARK 500 PRO D 49 -69.12 -29.53 REMARK 500 SER D 50 52.44 -102.01 REMARK 500 ILE D 55 -68.28 -95.87 REMARK 500 LYS D 74 -70.73 -107.31 REMARK 500 CYS D 105 -88.75 -96.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 6MKZ A 139 309 UNP P41274 TNFL9_MOUSE 139 309 DBREF 6MKZ B 24 160 UNP P20334 TNR9_MOUSE 24 160 DBREF 6MKZ C 139 309 UNP P41274 TNFL9_MOUSE 139 309 DBREF 6MKZ D 24 160 UNP P20334 TNR9_MOUSE 24 160 SEQADV 6MKZ ASP B 22 UNP P20334 EXPRESSION TAG SEQADV 6MKZ PRO B 23 UNP P20334 EXPRESSION TAG SEQADV 6MKZ ASP D 22 UNP P20334 EXPRESSION TAG SEQADV 6MKZ PRO D 23 UNP P20334 EXPRESSION TAG SEQRES 1 A 171 ASN THR THR GLN GLN GLY SER PRO VAL PHE ALA LYS LEU SEQRES 2 A 171 LEU ALA LYS ASN GLN ALA SER LEU CYS ASN THR THR LEU SEQRES 3 A 171 ASN TRP HIS SER GLN ASP GLY ALA GLY SER SER TYR LEU SEQRES 4 A 171 SER GLN GLY LEU ARG TYR GLU GLU ASP LYS LYS GLU LEU SEQRES 5 A 171 VAL VAL ASP SER PRO GLY LEU TYR TYR VAL PHE LEU GLU SEQRES 6 A 171 LEU LYS LEU SER PRO THR PHE THR ASN THR GLY HIS LYS SEQRES 7 A 171 VAL GLN GLY TRP VAL SER LEU VAL LEU GLN ALA LYS PRO SEQRES 8 A 171 GLN VAL ASP ASP PHE ASP ASN LEU ALA LEU THR VAL GLU SEQRES 9 A 171 LEU PHE PRO CYS SER MET GLU ASN LYS LEU VAL ASP ARG SEQRES 10 A 171 SER TRP SER GLN LEU LEU LEU LEU LYS ALA GLY HIS ARG SEQRES 11 A 171 LEU SER VAL GLY LEU ARG ALA TYR LEU HIS GLY ALA GLN SEQRES 12 A 171 ASP ALA TYR ARG ASP TRP GLU LEU SER TYR PRO ASN THR SEQRES 13 A 171 THR SER PHE GLY LEU PHE LEU VAL LYS PRO ASP ASN PRO SEQRES 14 A 171 TRP GLU SEQRES 1 B 139 ASP PRO VAL GLN ASN SER CYS ASP ASN CYS GLN PRO GLY SEQRES 2 B 139 THR PHE CYS ARG LYS TYR ASN PRO VAL CYS LYS SER CYS SEQRES 3 B 139 PRO PRO SER THR PHE SER SER ILE GLY GLY GLN PRO ASN SEQRES 4 B 139 CYS ASN ILE CYS ARG VAL CYS ALA GLY TYR PHE ARG PHE SEQRES 5 B 139 LYS LYS PHE CYS SER SER THR HIS ASN ALA GLU CYS GLU SEQRES 6 B 139 CYS ILE GLU GLY PHE HIS CYS LEU GLY PRO GLN CYS THR SEQRES 7 B 139 ARG CYS GLU LYS ASP CYS ARG PRO GLY GLN GLU LEU THR SEQRES 8 B 139 LYS GLN GLY CYS LYS THR CYS SER LEU GLY THR PHE ASN SEQRES 9 B 139 ASP GLN ASN GLY THR GLY VAL CYS ARG PRO TRP THR ASN SEQRES 10 B 139 CYS SER LEU ASP GLY ARG SER VAL LEU LYS THR GLY THR SEQRES 11 B 139 THR GLU LYS ASP VAL VAL CYS GLY PRO SEQRES 1 C 171 ASN THR THR GLN GLN GLY SER PRO VAL PHE ALA LYS LEU SEQRES 2 C 171 LEU ALA LYS ASN GLN ALA SER LEU CYS ASN THR THR LEU SEQRES 3 C 171 ASN TRP HIS SER GLN ASP GLY ALA GLY SER SER TYR LEU SEQRES 4 C 171 SER GLN GLY LEU ARG TYR GLU GLU ASP LYS LYS GLU LEU SEQRES 5 C 171 VAL VAL ASP SER PRO GLY LEU TYR TYR VAL PHE LEU GLU SEQRES 6 C 171 LEU LYS LEU SER PRO THR PHE THR ASN THR GLY HIS LYS SEQRES 7 C 171 VAL GLN GLY TRP VAL SER LEU VAL LEU GLN ALA LYS PRO SEQRES 8 C 171 GLN VAL ASP ASP PHE ASP ASN LEU ALA LEU THR VAL GLU SEQRES 9 C 171 LEU PHE PRO CYS SER MET GLU ASN LYS LEU VAL ASP ARG SEQRES 10 C 171 SER TRP SER GLN LEU LEU LEU LEU LYS ALA GLY HIS ARG SEQRES 11 C 171 LEU SER VAL GLY LEU ARG ALA TYR LEU HIS GLY ALA GLN SEQRES 12 C 171 ASP ALA TYR ARG ASP TRP GLU LEU SER TYR PRO ASN THR SEQRES 13 C 171 THR SER PHE GLY LEU PHE LEU VAL LYS PRO ASP ASN PRO SEQRES 14 C 171 TRP GLU SEQRES 1 D 139 ASP PRO VAL GLN ASN SER CYS ASP ASN CYS GLN PRO GLY SEQRES 2 D 139 THR PHE CYS ARG LYS TYR ASN PRO VAL CYS LYS SER CYS SEQRES 3 D 139 PRO PRO SER THR PHE SER SER ILE GLY GLY GLN PRO ASN SEQRES 4 D 139 CYS ASN ILE CYS ARG VAL CYS ALA GLY TYR PHE ARG PHE SEQRES 5 D 139 LYS LYS PHE CYS SER SER THR HIS ASN ALA GLU CYS GLU SEQRES 6 D 139 CYS ILE GLU GLY PHE HIS CYS LEU GLY PRO GLN CYS THR SEQRES 7 D 139 ARG CYS GLU LYS ASP CYS ARG PRO GLY GLN GLU LEU THR SEQRES 8 D 139 LYS GLN GLY CYS LYS THR CYS SER LEU GLY THR PHE ASN SEQRES 9 D 139 ASP GLN ASN GLY THR GLY VAL CYS ARG PRO TRP THR ASN SEQRES 10 D 139 CYS SER LEU ASP GLY ARG SER VAL LEU LYS THR GLY THR SEQRES 11 D 139 THR GLU LYS ASP VAL VAL CYS GLY PRO HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 5 NAG 4(C8 H15 N O6) FORMUL 5 BMA 2(C6 H12 O6) FORMUL 7 HOH *175(H2 O) HELIX 1 AA1 CYS A 246 ASN A 250 5 5 HELIX 2 AA2 ASP A 282 ARG A 285 5 4 HELIX 3 AA3 PHE C 244 ASN C 250 5 7 HELIX 4 AA4 ALA C 283 ARG C 285 5 3 SHEET 1 AA1 5 ASN A 165 HIS A 167 0 SHEET 2 AA1 5 PHE A 148 LYS A 154 -1 N LEU A 152 O HIS A 167 SHEET 3 AA1 5 SER A 296 PRO A 304 -1 O PHE A 297 N LEU A 151 SHEET 4 AA1 5 GLY A 196 PRO A 208 -1 N PHE A 201 O GLY A 298 SHEET 5 AA1 5 VAL A 253 LEU A 263 -1 O LEU A 261 N TYR A 198 SHEET 1 AA2 5 TYR A 176 LEU A 177 0 SHEET 2 AA2 5 PHE A 148 LYS A 154 -1 N LYS A 150 O TYR A 176 SHEET 3 AA2 5 SER A 296 PRO A 304 -1 O PHE A 297 N LEU A 151 SHEET 4 AA2 5 GLY A 196 PRO A 208 -1 N PHE A 201 O GLY A 298 SHEET 5 AA2 5 TRP A 287 LEU A 289 -1 O GLU A 288 N SER A 207 SHEET 1 AA3 4 THR A 162 THR A 163 0 SHEET 2 AA3 4 HIS A 267 HIS A 278 -1 O LEU A 273 N THR A 162 SHEET 3 AA3 4 GLU A 189 VAL A 192 -1 N LEU A 190 O LEU A 269 SHEET 4 AA3 4 LEU A 181 GLU A 184 -1 N GLU A 184 O GLU A 189 SHEET 1 AA4 4 THR A 162 THR A 163 0 SHEET 2 AA4 4 HIS A 267 HIS A 278 -1 O LEU A 273 N THR A 162 SHEET 3 AA4 4 GLN A 218 ALA A 227 -1 N SER A 222 O ARG A 274 SHEET 4 AA4 4 LEU A 239 LEU A 243 -1 O LEU A 243 N GLY A 219 SHEET 1 AA5 2 THR B 35 PHE B 36 0 SHEET 2 AA5 2 LYS B 45 SER B 46 -1 O LYS B 45 N PHE B 36 SHEET 1 AA6 2 THR B 51 PHE B 52 0 SHEET 2 AA6 2 ASN B 62 ILE B 63 -1 O ASN B 62 N PHE B 52 SHEET 1 AA7 2 PHE B 71 LYS B 75 0 SHEET 2 AA7 2 GLU B 84 CYS B 87 -1 O GLU B 86 N ARG B 72 SHEET 1 AA8 2 PHE B 91 LEU B 94 0 SHEET 2 AA8 2 ARG B 100 LYS B 103 -1 O GLU B 102 N HIS B 92 SHEET 1 AA9 2 GLN B 109 GLU B 110 0 SHEET 2 AA9 2 LYS B 117 THR B 118 -1 O LYS B 117 N GLU B 110 SHEET 1 AB1 5 ASN C 165 HIS C 167 0 SHEET 2 AB1 5 PHE C 148 LYS C 154 -1 N LEU C 152 O HIS C 167 SHEET 3 AB1 5 SER C 296 PRO C 304 -1 O PHE C 297 N LEU C 151 SHEET 4 AB1 5 GLY C 196 PRO C 208 -1 N PHE C 201 O GLY C 298 SHEET 5 AB1 5 VAL C 253 LEU C 263 -1 O LEU C 261 N TYR C 198 SHEET 1 AB2 5 TYR C 176 LEU C 177 0 SHEET 2 AB2 5 PHE C 148 LYS C 154 -1 N LYS C 150 O TYR C 176 SHEET 3 AB2 5 SER C 296 PRO C 304 -1 O PHE C 297 N LEU C 151 SHEET 4 AB2 5 GLY C 196 PRO C 208 -1 N PHE C 201 O GLY C 298 SHEET 5 AB2 5 TRP C 287 LEU C 289 -1 O GLU C 288 N SER C 207 SHEET 1 AB3 4 THR C 162 THR C 163 0 SHEET 2 AB3 4 HIS C 267 HIS C 278 -1 O LEU C 273 N THR C 162 SHEET 3 AB3 4 GLU C 189 VAL C 192 -1 N LEU C 190 O LEU C 269 SHEET 4 AB3 4 LEU C 181 GLU C 184 -1 N ARG C 182 O VAL C 191 SHEET 1 AB4 4 THR C 162 THR C 163 0 SHEET 2 AB4 4 HIS C 267 HIS C 278 -1 O LEU C 273 N THR C 162 SHEET 3 AB4 4 GLN C 218 LYS C 228 -1 N SER C 222 O ARG C 274 SHEET 4 AB4 4 ALA C 238 LEU C 243 -1 O LEU C 243 N GLY C 219 SHEET 1 AB5 2 THR D 35 PHE D 36 0 SHEET 2 AB5 2 LYS D 45 SER D 46 -1 O LYS D 45 N PHE D 36 SHEET 1 AB6 2 THR D 51 PHE D 52 0 SHEET 2 AB6 2 ASN D 62 ILE D 63 -1 O ASN D 62 N PHE D 52 SHEET 1 AB7 2 PHE D 71 LYS D 75 0 SHEET 2 AB7 2 GLU D 84 CYS D 87 -1 O GLU D 86 N ARG D 72 SHEET 1 AB8 2 PHE D 91 LEU D 94 0 SHEET 2 AB8 2 ARG D 100 LYS D 103 -1 O GLU D 102 N HIS D 92 SSBOND 1 CYS A 246 CYS C 246 1555 1555 2.04 SSBOND 2 CYS B 28 CYS B 37 1555 1555 2.05 SSBOND 3 CYS B 31 CYS B 44 1555 1555 1.93 SSBOND 4 CYS B 47 CYS B 61 1555 1555 2.07 SSBOND 5 CYS B 64 CYS B 77 1555 1555 1.97 SSBOND 6 CYS B 67 CYS B 85 1555 1555 2.04 SSBOND 7 CYS B 87 CYS B 101 1555 1555 2.04 SSBOND 8 CYS B 93 CYS B 98 1555 1555 2.06 SSBOND 9 CYS B 105 CYS B 116 1555 1555 2.06 SSBOND 10 CYS B 119 CYS B 133 1555 1555 2.03 SSBOND 11 CYS D 28 CYS D 37 1555 1555 1.87 SSBOND 12 CYS D 31 CYS D 44 1555 1555 2.20 SSBOND 13 CYS D 47 CYS D 61 1555 1555 2.05 SSBOND 14 CYS D 64 CYS D 77 1555 1555 2.02 SSBOND 15 CYS D 67 CYS D 85 1555 1555 2.04 SSBOND 16 CYS D 87 CYS D 101 1555 1555 2.04 SSBOND 17 CYS D 93 CYS D 98 1555 1555 2.04 LINK ND2 ASN A 161 C1 NAG E 1 1555 1555 1.43 LINK ND2 ASN C 161 C1 NAG F 1 1555 1555 1.43 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.41 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.42 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.40 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.41 CISPEP 1 TYR A 291 PRO A 292 0 3.38 CISPEP 2 LYS C 228 PRO C 229 0 1.76 CISPEP 3 TYR C 291 PRO C 292 0 3.09 CRYST1 61.499 88.478 155.158 90.00 90.00 90.00 P 21 21 21 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 0.016260 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006445 0.00000