HEADER CYTOKINE/SIGNALING PROTEIN 12-MAR-12 4E4D TITLE CRYSTAL STRUCTURE OF MOUSE RANKL-OPG COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11, SOLUBLE COMPND 3 FORM; COMPND 4 CHAIN: X; COMPND 5 FRAGMENT: UNP RESIDUES 162-316; COMPND 6 SYNONYM: OSTEOCLAST DIFFERENTIATION FACTOR, ODF, OSTEOPROTEGERIN COMPND 7 LIGAND, OPGL, RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA-B LIGAND, COMPND 8 RANKL, TNF-RELATED ACTIVATION-INDUCED CYTOKINE, TRANCE,; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11B; COMPND 12 CHAIN: R; COMPND 13 FRAGMENT: UNP RESIDUES 22-197; COMPND 14 SYNONYM: OSTEOCLASTOGENESIS INHIBITORY FACTOR, OSTEOPROTEGERIN; COMPND 15 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: CD254, ODF, OPGL, RANKL, TNFSF11, TRANCE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21CODONPLUS(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 STRAIN: C57BL/6 B; SOURCE 16 GENE: OCIF, OPG, OSTEOPROTEGERIN, TNFRSF11B; SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: HIGH FIVE; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: TRANSFER PLASMID; SOURCE 21 EXPRESSION_SYSTEM_VECTOR: BACULOVIRUS KEYWDS TNF-RELATED ACTIVATION-INDUCED CYTOKINE-RECEPTOR, CYSTEINE-RICH KEYWDS 2 DOMAIN, JELLY-ROLL FOLD, CYTOKINE-SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.A.NELSON,D.H.FREMONT REVDAT 4 13-SEP-23 4E4D 1 REMARK SEQADV REVDAT 3 15-NOV-17 4E4D 1 REMARK REVDAT 2 12-DEC-12 4E4D 1 JRNL REVDAT 1 24-OCT-12 4E4D 0 JRNL AUTH C.A.NELSON,J.T.WARREN,M.W.WANG,S.L.TEITELBAUM,D.H.FREMONT JRNL TITL RANKL EMPLOYS DISTINCT BINDING MODES TO ENGAGE RANK AND THE JRNL TITL 2 OSTEOPROTEGERIN DECOY RECEPTOR. JRNL REF STRUCTURE V. 20 1971 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 23039992 JRNL DOI 10.1016/J.STR.2012.08.030 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 14542 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1476 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 40.7034 - 5.9989 0.95 1178 162 0.2367 0.2660 REMARK 3 2 5.9989 - 4.7639 0.99 1228 123 0.1925 0.2210 REMARK 3 3 4.7639 - 4.1624 0.99 1209 157 0.1611 0.1830 REMARK 3 4 4.1624 - 3.7821 0.98 1203 130 0.1704 0.2332 REMARK 3 5 3.7821 - 3.5112 1.00 1202 148 0.1840 0.2310 REMARK 3 6 3.5112 - 3.3043 0.99 1212 117 0.2008 0.2193 REMARK 3 7 3.3043 - 3.1389 0.99 1209 130 0.2075 0.2623 REMARK 3 8 3.1389 - 3.0023 0.97 1178 133 0.2078 0.2501 REMARK 3 9 3.0023 - 2.8867 0.96 1172 135 0.2209 0.2817 REMARK 3 10 2.8867 - 2.7871 0.95 1164 114 0.2338 0.2840 REMARK 3 11 2.7871 - 2.7000 0.92 1111 127 0.2377 0.2833 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.12 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 2348 REMARK 3 ANGLE : 0.593 3171 REMARK 3 CHIRALITY : 0.040 336 REMARK 3 PLANARITY : 0.003 411 REMARK 3 DIHEDRAL : 9.943 852 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN R AND RESID 7:39) REMARK 3 ORIGIN FOR THE GROUP (A): 66.6807 -1.0808 27.5509 REMARK 3 T TENSOR REMARK 3 T11: 1.1839 T22: 0.8077 REMARK 3 T33: 0.6357 T12: 0.0909 REMARK 3 T13: -0.1425 T23: 0.1274 REMARK 3 L TENSOR REMARK 3 L11: 8.5775 L22: 2.8355 REMARK 3 L33: 2.6150 L12: 1.5397 REMARK 3 L13: -2.2381 L23: 0.7563 REMARK 3 S TENSOR REMARK 3 S11: 0.6831 S12: -1.3538 S13: -0.4485 REMARK 3 S21: 0.2598 S22: -0.4248 S23: -0.2471 REMARK 3 S31: 1.1337 S32: 1.2059 S33: -0.3246 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN R AND RESID 40:88) REMARK 3 ORIGIN FOR THE GROUP (A): 58.6539 2.4119 4.5034 REMARK 3 T TENSOR REMARK 3 T11: 1.2571 T22: 0.5755 REMARK 3 T33: 0.7069 T12: 0.0809 REMARK 3 T13: 0.0459 T23: -0.0340 REMARK 3 L TENSOR REMARK 3 L11: 0.5559 L22: 2.2446 REMARK 3 L33: 3.6470 L12: 0.0930 REMARK 3 L13: 1.3943 L23: -0.3416 REMARK 3 S TENSOR REMARK 3 S11: 0.0777 S12: 0.1495 S13: -0.2255 REMARK 3 S21: 0.0877 S22: -0.2212 S23: 0.0757 REMARK 3 S31: 1.4948 S32: 0.5157 S33: 0.1358 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN R AND RESID 89:121) REMARK 3 ORIGIN FOR THE GROUP (A): 68.7473 10.8470 -18.4317 REMARK 3 T TENSOR REMARK 3 T11: 1.0908 T22: 1.1385 REMARK 3 T33: 0.8206 T12: 0.1073 REMARK 3 T13: 0.2499 T23: -0.2232 REMARK 3 L TENSOR REMARK 3 L11: 4.5249 L22: 2.9653 REMARK 3 L33: 6.6838 L12: -0.1382 REMARK 3 L13: -4.0095 L23: 0.0742 REMARK 3 S TENSOR REMARK 3 S11: -0.0658 S12: 0.5958 S13: 0.2261 REMARK 3 S21: -0.9342 S22: 0.5103 S23: -1.4353 REMARK 3 S31: 0.9482 S32: 1.9733 S33: -0.3192 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN R AND RESID 122:125) REMARK 3 ORIGIN FOR THE GROUP (A): 82.8869 11.2919 -29.3658 REMARK 3 T TENSOR REMARK 3 T11: 1.7367 T22: 2.5570 REMARK 3 T33: 1.1461 T12: -0.5512 REMARK 3 T13: 0.5491 T23: -0.5889 REMARK 3 L TENSOR REMARK 3 L11: 0.2621 L22: 8.1575 REMARK 3 L33: 6.0877 L12: -1.4365 REMARK 3 L13: 0.6996 L23: -2.7393 REMARK 3 S TENSOR REMARK 3 S11: 0.5490 S12: 0.5597 S13: 0.0664 REMARK 3 S21: -1.4366 S22: -1.0267 S23: -0.4104 REMARK 3 S31: 0.9980 S32: 0.5623 S33: 0.0501 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN R AND RESID 126:141) REMARK 3 ORIGIN FOR THE GROUP (A): 76.5962 7.6354 -33.8245 REMARK 3 T TENSOR REMARK 3 T11: 1.3552 T22: 1.4101 REMARK 3 T33: 1.3504 T12: -0.1326 REMARK 3 T13: 0.3453 T23: -0.0366 REMARK 3 L TENSOR REMARK 3 L11: 6.4417 L22: 4.8215 REMARK 3 L33: 4.8081 L12: -5.5088 REMARK 3 L13: -4.3510 L23: 4.1762 REMARK 3 S TENSOR REMARK 3 S11: -0.0515 S12: -0.0599 S13: 0.2790 REMARK 3 S21: 0.3516 S22: 0.4126 S23: -0.3805 REMARK 3 S31: -0.5967 S32: 0.1375 S33: -0.5055 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN X AND RESID 162:179) REMARK 3 ORIGIN FOR THE GROUP (A): 72.1510 29.2634 4.8917 REMARK 3 T TENSOR REMARK 3 T11: 0.3580 T22: 0.5204 REMARK 3 T33: 0.6134 T12: 0.0008 REMARK 3 T13: -0.0400 T23: 0.0613 REMARK 3 L TENSOR REMARK 3 L11: 4.0371 L22: 9.1108 REMARK 3 L33: 8.6848 L12: 0.8070 REMARK 3 L13: 5.3166 L23: 1.4757 REMARK 3 S TENSOR REMARK 3 S11: 0.1231 S12: 0.7271 S13: -0.5028 REMARK 3 S21: -0.6051 S22: 0.1119 S23: -1.1943 REMARK 3 S31: 0.5268 S32: 1.6495 S33: -0.2257 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN X AND RESID 180:226) REMARK 3 ORIGIN FOR THE GROUP (A): 69.5004 28.7157 7.9360 REMARK 3 T TENSOR REMARK 3 T11: 0.3024 T22: 0.5735 REMARK 3 T33: 0.3619 T12: 0.0097 REMARK 3 T13: 0.0102 T23: 0.0510 REMARK 3 L TENSOR REMARK 3 L11: 2.8013 L22: 3.7780 REMARK 3 L33: 3.3380 L12: 0.2372 REMARK 3 L13: -0.6458 L23: -0.0455 REMARK 3 S TENSOR REMARK 3 S11: 0.0219 S12: -0.1710 S13: -0.3190 REMARK 3 S21: 0.2644 S22: -0.1318 S23: -0.5742 REMARK 3 S31: 0.2375 S32: 1.2025 S33: 0.1355 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN X AND RESID 227:232) REMARK 3 ORIGIN FOR THE GROUP (A): 68.2566 31.4592 -25.0154 REMARK 3 T TENSOR REMARK 3 T11: 1.6324 T22: 2.1203 REMARK 3 T33: 0.9474 T12: -0.4565 REMARK 3 T13: 0.2910 T23: 0.0750 REMARK 3 L TENSOR REMARK 3 L11: 2.0000 L22: 6.0610 REMARK 3 L33: 6.3118 L12: 7.6293 REMARK 3 L13: -5.7892 L23: -5.5645 REMARK 3 S TENSOR REMARK 3 S11: 0.9090 S12: -0.8568 S13: 1.0134 REMARK 3 S21: 1.3388 S22: 0.3576 S23: 0.2483 REMARK 3 S31: -1.0930 S32: -0.2267 S33: -1.1278 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN X AND RESID 233:266) REMARK 3 ORIGIN FOR THE GROUP (A): 63.0837 20.9015 -2.4835 REMARK 3 T TENSOR REMARK 3 T11: 0.4292 T22: 0.2559 REMARK 3 T33: 0.3406 T12: 0.0097 REMARK 3 T13: 0.0655 T23: -0.0831 REMARK 3 L TENSOR REMARK 3 L11: 5.6644 L22: 4.7526 REMARK 3 L33: 3.5115 L12: 0.8088 REMARK 3 L13: -0.2015 L23: 0.6604 REMARK 3 S TENSOR REMARK 3 S11: 0.0375 S12: 0.4758 S13: -0.5162 REMARK 3 S21: -0.5537 S22: -0.1493 S23: -0.2563 REMARK 3 S31: 0.7509 S32: 0.7274 S33: 0.2082 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN X AND RESID 267:315) REMARK 3 ORIGIN FOR THE GROUP (A): 64.2693 28.0275 4.7835 REMARK 3 T TENSOR REMARK 3 T11: 0.1489 T22: 0.3046 REMARK 3 T33: 0.3058 T12: 0.0060 REMARK 3 T13: -0.0280 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 2.5824 L22: 4.4716 REMARK 3 L33: 4.9911 L12: 0.0776 REMARK 3 L13: -0.0368 L23: 0.6420 REMARK 3 S TENSOR REMARK 3 S11: -0.0348 S12: -0.0523 S13: 0.0026 REMARK 3 S21: 0.0052 S22: -0.0134 S23: -0.0507 REMARK 3 S31: 0.2050 S32: 0.6225 S33: 0.0630 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 4E4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071153. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9951 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14915 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56300 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: SHARP REMARK 200 STARTING MODEL: PDB ENTRY 1JTZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM PHOSPHATE/CITRATE REMARK 280 BUFFER, 14% POLYETHYLENE GLYCOL 8000 AND 250 MM SODIUM CHLORIDE, REMARK 280 PH 4.10, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.40000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.40000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.40000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X REMARK 350 BIOMT1 1 -0.500000 0.866025 0.000000 54.88150 REMARK 350 BIOMT2 1 -0.866025 -0.500000 0.000000 95.05755 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, R REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 109.76300 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -111.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, R 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 -0.500000 -0.866025 0.000000 109.76300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 54.88150 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 95.05755 REMARK 350 BIOMT3 3 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 ASP X 316 REMARK 465 GLU R 1 REMARK 465 THR R 2 REMARK 465 LEU R 3 REMARK 465 PRO R 4 REMARK 465 PRO R 5 REMARK 465 LYS R 6 REMARK 465 HIS R 142 REMARK 465 THR R 143 REMARK 465 ASN R 144 REMARK 465 CYS R 145 REMARK 465 SER R 146 REMARK 465 THR R 147 REMARK 465 PHE R 148 REMARK 465 GLY R 149 REMARK 465 LEU R 150 REMARK 465 LEU R 151 REMARK 465 LEU R 152 REMARK 465 ILE R 153 REMARK 465 GLN R 154 REMARK 465 LYS R 155 REMARK 465 GLY R 156 REMARK 465 ASN R 157 REMARK 465 ALA R 158 REMARK 465 THR R 159 REMARK 465 HIS R 160 REMARK 465 ASP R 161 REMARK 465 ASN R 162 REMARK 465 VAL R 163 REMARK 465 CYS R 164 REMARK 465 SER R 165 REMARK 465 GLY R 166 REMARK 465 ASN R 167 REMARK 465 ARG R 168 REMARK 465 GLU R 169 REMARK 465 ALA R 170 REMARK 465 THR R 171 REMARK 465 GLN R 172 REMARK 465 LYS R 173 REMARK 465 CYS R 174 REMARK 465 GLY R 175 REMARK 465 ILE R 176 REMARK 465 ALA R 177 REMARK 465 SER R 178 REMARK 465 SER R 179 REMARK 465 VAL R 180 REMARK 465 LEU R 181 REMARK 465 PRO R 182 REMARK 465 ARG R 183 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 O LYS R 122 O HOH R 220 2.11 REMARK 500 O HOH R 214 O HOH R 218 2.18 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 SER X 176 68.88 -113.94 REMARK 500 ASP X 189 49.57 -156.06 REMARK 500 PRO X 249 106.20 -59.53 REMARK 500 SER X 264 -168.21 -69.94 REMARK 500 TYR R 10 -161.92 -128.03 REMARK 500 ASP R 11 117.20 -161.89 REMARK 500 THR R 14 -68.11 -147.93 REMARK 500 HIS R 16 125.22 -175.73 REMARK 500 LEU R 69 38.62 -98.45 REMARK 500 GLU R 87 173.97 -57.97 REMARK 500 ILE R 94 -91.82 60.79 REMARK 500 PRO R 115 -3.90 -59.39 REMARK 500 LYS R 136 45.67 -144.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL X 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL X 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ME2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MOUSE RANKL-RANK COMPLEX REMARK 900 RELATED ID: 3QBQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF EXTRACELLULAR DOMAINS OF MOUSE RANK-RANKL REMARK 900 COMPLEX REMARK 900 RELATED ID: 3ALQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TNF-TNFR2 COMPLEX REMARK 900 RELATED ID: 3K51 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DCR3-TL1A COMPLEX REMARK 900 RELATED ID: 3QO4 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF DEATH RECEPTOR 6 REMARK 900 RELATED ID: 1TNR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SOLUBLE HUMAN 55 KD TNF RECEPTOR-HUMAN TNF- REMARK 900 BETA COMPLEX: IMPLICATIONS FOR TNF RECEPTOR ACTIVATION DBREF 4E4D X 162 316 UNP O35235 TNF11_MOUSE 162 316 DBREF 4E4D R 1 176 UNP O08712 TR11B_MOUSE 22 197 SEQADV 4E4D ALA R 177 UNP O08712 EXPRESSION TAG SEQADV 4E4D SER R 178 UNP O08712 EXPRESSION TAG SEQADV 4E4D SER R 179 UNP O08712 EXPRESSION TAG SEQADV 4E4D VAL R 180 UNP O08712 EXPRESSION TAG SEQADV 4E4D LEU R 181 UNP O08712 EXPRESSION TAG SEQADV 4E4D PRO R 182 UNP O08712 EXPRESSION TAG SEQADV 4E4D ARG R 183 UNP O08712 EXPRESSION TAG SEQRES 1 X 155 GLN PRO PHE ALA HIS LEU THR ILE ASN ALA ALA SER ILE SEQRES 2 X 155 PRO SER GLY SER HIS LYS VAL THR LEU SER SER TRP TYR SEQRES 3 X 155 HIS ASP ARG GLY TRP ALA LYS ILE SER ASN MET THR LEU SEQRES 4 X 155 SER ASN GLY LYS LEU ARG VAL ASN GLN ASP GLY PHE TYR SEQRES 5 X 155 TYR LEU TYR ALA ASN ILE CYS PHE ARG HIS HIS GLU THR SEQRES 6 X 155 SER GLY SER VAL PRO THR ASP TYR LEU GLN LEU MET VAL SEQRES 7 X 155 TYR VAL VAL LYS THR SER ILE LYS ILE PRO SER SER HIS SEQRES 8 X 155 ASN LEU MET LYS GLY GLY SER THR LYS ASN TRP SER GLY SEQRES 9 X 155 ASN SER GLU PHE HIS PHE TYR SER ILE ASN VAL GLY GLY SEQRES 10 X 155 PHE PHE LYS LEU ARG ALA GLY GLU GLU ILE SER ILE GLN SEQRES 11 X 155 VAL SER ASN PRO SER LEU LEU ASP PRO ASP GLN ASP ALA SEQRES 12 X 155 THR TYR PHE GLY ALA PHE LYS VAL GLN ASP ILE ASP SEQRES 1 R 183 GLU THR LEU PRO PRO LYS TYR LEU HIS TYR ASP PRO GLU SEQRES 2 R 183 THR GLY HIS GLN LEU LEU CYS ASP LYS CYS ALA PRO GLY SEQRES 3 R 183 THR TYR LEU LYS GLN HIS CYS THR VAL ARG ARG LYS THR SEQRES 4 R 183 LEU CYS VAL PRO CYS PRO ASP HIS SER TYR THR ASP SER SEQRES 5 R 183 TRP HIS THR SER ASP GLU CYS VAL TYR CYS SER PRO VAL SEQRES 6 R 183 CYS LYS GLU LEU GLN SER VAL LYS GLN GLU CYS ASN ARG SEQRES 7 R 183 THR HIS ASN ARG VAL CYS GLU CYS GLU GLU GLY ARG TYR SEQRES 8 R 183 LEU GLU ILE GLU PHE CYS LEU LYS HIS ARG SER CYS PRO SEQRES 9 R 183 PRO GLY SER GLY VAL VAL GLN ALA GLY THR PRO GLU ARG SEQRES 10 R 183 ASN THR VAL CYS LYS LYS CYS PRO ASP GLY PHE PHE SER SEQRES 11 R 183 GLY GLU THR SER SER LYS ALA PRO CYS ILE LYS HIS THR SEQRES 12 R 183 ASN CYS SER THR PHE GLY LEU LEU LEU ILE GLN LYS GLY SEQRES 13 R 183 ASN ALA THR HIS ASP ASN VAL CYS SER GLY ASN ARG GLU SEQRES 14 R 183 ALA THR GLN LYS CYS GLY ILE ALA SER SER VAL LEU PRO SEQRES 15 R 183 ARG HET CL X 401 1 HET CL X 402 1 HETNAM CL CHLORIDE ION FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *93(H2 O) HELIX 1 1 ASN X 294 LEU X 298 5 5 SHEET 1 A 3 TRP X 186 TYR X 187 0 SHEET 2 A 3 PHE X 164 ILE X 169 -1 N THR X 168 O TYR X 187 SHEET 3 A 3 LYS X 194 SER X 196 -1 O LYS X 194 N HIS X 166 SHEET 1 B 5 TRP X 186 TYR X 187 0 SHEET 2 B 5 PHE X 164 ILE X 169 -1 N THR X 168 O TYR X 187 SHEET 3 B 5 TYR X 306 GLN X 313 -1 O PHE X 307 N LEU X 167 SHEET 4 B 5 GLY X 211 HIS X 224 -1 N ASN X 218 O TYR X 306 SHEET 5 B 5 PHE X 269 LEU X 282 -1 O TYR X 272 N PHE X 221 SHEET 1 C 4 VAL X 181 THR X 182 0 SHEET 2 C 4 GLU X 287 VAL X 292 -1 O VAL X 292 N VAL X 181 SHEET 3 C 4 LYS X 204 VAL X 207 -1 N LEU X 205 O ILE X 288 SHEET 4 C 4 MET X 198 SER X 201 -1 N THR X 199 O ARG X 206 SHEET 1 D 4 VAL X 181 THR X 182 0 SHEET 2 D 4 GLU X 287 VAL X 292 -1 O VAL X 292 N VAL X 181 SHEET 3 D 4 TYR X 234 THR X 244 -1 N VAL X 242 O SER X 289 SHEET 4 D 4 SER X 251 ASN X 262 -1 O LEU X 254 N VAL X 241 SHEET 1 E 2 HIS R 9 TYR R 10 0 SHEET 2 E 2 CYS R 20 ASP R 21 -1 O CYS R 20 N TYR R 10 SHEET 1 F 2 THR R 27 GLN R 31 0 SHEET 2 F 2 LEU R 40 PRO R 43 -1 O VAL R 42 N TYR R 28 SHEET 1 G 2 SER R 48 TYR R 49 0 SHEET 2 G 2 VAL R 60 TYR R 61 -1 O VAL R 60 N TYR R 49 SHEET 1 H 2 GLN R 70 GLN R 74 0 SHEET 2 H 2 VAL R 83 CYS R 86 -1 O GLU R 85 N SER R 71 SHEET 1 I 2 ARG R 90 GLU R 93 0 SHEET 2 I 2 PHE R 96 LYS R 99 -1 O PHE R 96 N GLU R 93 SHEET 1 J 2 SER R 107 GLN R 111 0 SHEET 2 J 2 VAL R 120 LYS R 123 -1 O VAL R 120 N VAL R 110 SSBOND 1 CYS R 20 CYS R 33 1555 1555 2.03 SSBOND 2 CYS R 23 CYS R 41 1555 1555 2.04 SSBOND 3 CYS R 44 CYS R 59 1555 1555 2.04 SSBOND 4 CYS R 62 CYS R 76 1555 1555 2.03 SSBOND 5 CYS R 66 CYS R 84 1555 1555 2.03 SSBOND 6 CYS R 86 CYS R 97 1555 1555 2.03 SSBOND 7 CYS R 103 CYS R 121 1555 1555 2.03 SSBOND 8 CYS R 124 CYS R 139 1555 1555 2.03 CISPEP 1 SER R 63 PRO R 64 0 0.31 SITE 1 AC1 6 SER X 185 TRP X 186 LEU X 200 ASN X 202 SITE 2 AC1 6 GLY X 203 HOH X 526 SITE 1 AC2 3 HIS X 188 ASP X 189 ARG X 190 CRYST1 109.763 109.763 78.800 90.00 90.00 120.00 P 63 6 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 0.009111 0.005260 0.000000 0.00000 SCALE2 0.000000 0.010520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012690 0.00000