HEADER CYTOKINE/CYTOKINE RECEPTOR 31-MAR-10 3ME2 TITLE CRYSTAL STRUCTURE OF MOUSE RANKL-RANK COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 158-316; COMPND 5 SYNONYM: RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA-B LIGAND, RANKL, COMPND 6 TNF-RELATED ACTIVATION-INDUCED CYTOKINE, TRANCE, OSTEOPROTEGERIN COMPND 7 LIGAND, OPGL, OSTEOCLAST DIFFERENTIATION FACTOR, ODF; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11A; COMPND 11 CHAIN: R; COMPND 12 FRAGMENT: UNP RESIDUES 26-210; COMPND 13 SYNONYM: RECEPTOR ACTIVATOR OF NF-KB, OSTEOCLAST DIFFERENTIATION COMPND 14 FACTOR RECEPTOR, ODFR, RANK; 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: OPGL, RANKL, TNFSF11, TRANCE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 OTHER_DETAILS: RAW264.7; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 14 ORGANISM_COMMON: MOUSE; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 GENE: RANK, TNFRSF11A; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3); SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 22 OTHER_DETAILS: RAW264.7 KEYWDS RANK, RANKL, RANKL-RANK COMPLEX, TNFSF11, TNFRSF11A, TNF SUPERFAMILY, KEYWDS 2 CYTOKINE-CYTOKINE RECEPTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.W.WALTER,C.Z.LIU,X.K.ZHU,Y.WU,R.J.OWENS,D.I.STUART,B.GAO,J.REN REVDAT 3 13-NOV-24 3ME2 1 REMARK REVDAT 2 01-NOV-23 3ME2 1 REMARK SEQADV LINK REVDAT 1 02-JUN-10 3ME2 0 JRNL AUTH C.LIU,T.S.WALTER,P.HUANG,S.ZHANG,X.ZHU,Y.WU,L.R.WEDDERBURN, JRNL AUTH 2 P.TANG,R.J.OWENS,D.I.STUART,J.REN,B.GAO JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS OF RANKL-RANK INTERACTION JRNL TITL 2 AND SIGNALING. JRNL REF J.IMMUNOL. 2010 JRNL REFN ISSN 0022-1767 JRNL PMID 20483727 JRNL DOI 10.4049/JIMMUNOL.0904033 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 17956 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 995 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1298 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2494 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.21000 REMARK 3 B22 (A**2) : 2.21000 REMARK 3 B33 (A**2) : -3.31000 REMARK 3 B12 (A**2) : 1.10000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.273 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.051 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2570 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3494 ; 0.999 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 5.741 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;33.822 ;24.174 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 407 ;13.798 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.316 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 373 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1966 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1602 ; 1.203 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2582 ; 2.271 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 968 ; 2.353 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 912 ; 3.691 ;10.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 161 A 316 REMARK 3 ORIGIN FOR THE GROUP (A): 59.1340 47.7860 47.3450 REMARK 3 T TENSOR REMARK 3 T11: 0.1477 T22: 0.0372 REMARK 3 T33: 0.0912 T12: -0.0019 REMARK 3 T13: 0.0359 T23: -0.0312 REMARK 3 L TENSOR REMARK 3 L11: 3.5185 L22: 1.9285 REMARK 3 L33: 2.6253 L12: -0.2932 REMARK 3 L13: 0.1957 L23: -0.1160 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: -0.1718 S13: 0.2600 REMARK 3 S21: 0.0847 S22: 0.0529 S23: -0.1020 REMARK 3 S31: -0.5548 S32: 0.0285 S33: -0.0550 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 34 R 89 REMARK 3 ORIGIN FOR THE GROUP (A): 82.5860 57.2400 64.5160 REMARK 3 T TENSOR REMARK 3 T11: 0.3946 T22: 0.6031 REMARK 3 T33: 0.4173 T12: -0.0299 REMARK 3 T13: -0.0099 T23: -0.1817 REMARK 3 L TENSOR REMARK 3 L11: 4.2848 L22: 3.1858 REMARK 3 L33: 18.8774 L12: 1.4925 REMARK 3 L13: 3.1165 L23: 5.4643 REMARK 3 S TENSOR REMARK 3 S11: -0.1117 S12: -0.7243 S13: 0.8576 REMARK 3 S21: -0.0359 S22: 0.1212 S23: 0.2722 REMARK 3 S31: -1.4280 S32: -0.8901 S33: -0.0096 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 90 R 116 REMARK 3 ORIGIN FOR THE GROUP (A): 84.8510 50.0720 40.8720 REMARK 3 T TENSOR REMARK 3 T11: 0.1756 T22: 0.4526 REMARK 3 T33: 0.2646 T12: -0.1346 REMARK 3 T13: 0.0489 T23: -0.1110 REMARK 3 L TENSOR REMARK 3 L11: 1.3042 L22: 0.6583 REMARK 3 L33: 14.5657 L12: 0.8975 REMARK 3 L13: 1.8492 L23: 1.6882 REMARK 3 S TENSOR REMARK 3 S11: 0.0218 S12: -0.1168 S13: 0.1599 REMARK 3 S21: -0.0495 S22: 0.0283 S23: 0.0343 REMARK 3 S31: -0.7033 S32: 0.5584 S33: -0.0501 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 117 R 172 REMARK 3 ORIGIN FOR THE GROUP (A): 78.2760 58.1870 18.3580 REMARK 3 T TENSOR REMARK 3 T11: 0.2399 T22: 0.3292 REMARK 3 T33: 0.2384 T12: -0.0381 REMARK 3 T13: 0.1026 T23: 0.0438 REMARK 3 L TENSOR REMARK 3 L11: 2.0245 L22: 2.9637 REMARK 3 L33: 12.1268 L12: 1.9376 REMARK 3 L13: -2.6692 L23: -5.6000 REMARK 3 S TENSOR REMARK 3 S11: 0.2149 S12: 0.1055 S13: 0.1158 REMARK 3 S21: 0.3829 S22: -0.0198 S23: 0.0610 REMARK 3 S31: -0.7594 S32: -0.0297 S33: -0.1951 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 173 R 199 REMARK 3 ORIGIN FOR THE GROUP (A): 85.3760 63.1010 -7.2700 REMARK 3 T TENSOR REMARK 3 T11: 0.3033 T22: 0.5773 REMARK 3 T33: 0.2728 T12: 0.0163 REMARK 3 T13: -0.0563 T23: 0.0493 REMARK 3 L TENSOR REMARK 3 L11: 14.3712 L22: 3.0408 REMARK 3 L33: 12.3221 L12: -2.6250 REMARK 3 L13: -9.0788 L23: -1.2636 REMARK 3 S TENSOR REMARK 3 S11: 0.4750 S12: 1.6897 S13: 0.4456 REMARK 3 S21: -0.4489 S22: -0.0412 S23: 0.3184 REMARK 3 S31: -0.6313 S32: -1.6414 S33: -0.4338 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3ME2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058429. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-07; 15-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF REMARK 200 BEAMLINE : ID14-4; ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9395; 0.8726 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; MARMOSAIC 225 REMARK 200 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18587 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 16.30 REMARK 200 R MERGE (I) : 0.19100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.80 REMARK 200 R MERGE FOR SHELL (I) : 0.99500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1JTZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM DI-HYDROGEN PHOSPHATE, 2M REMARK 280 SODIUM CHLORIDE, 0.1M POTASSIUM DI-HYDROGEN PHOSPHATE, 0.1M MES, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 47.49750 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 47.49750 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 47.49750 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 121.22500 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 60.61250 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 104.98393 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 GLY A 146 REMARK 465 PRO A 147 REMARK 465 LEU A 148 REMARK 465 GLY A 149 REMARK 465 SER A 150 REMARK 465 PRO A 151 REMARK 465 GLU A 152 REMARK 465 PHE A 153 REMARK 465 PRO A 154 REMARK 465 GLY A 155 REMARK 465 ARG A 156 REMARK 465 ARG A 157 REMARK 465 LYS A 158 REMARK 465 PRO A 159 REMARK 465 GLU A 160 REMARK 465 MET R 3 REMARK 465 GLY R 4 REMARK 465 SER R 5 REMARK 465 SER R 6 REMARK 465 HIS R 7 REMARK 465 HIS R 8 REMARK 465 HIS R 9 REMARK 465 HIS R 10 REMARK 465 HIS R 11 REMARK 465 HIS R 12 REMARK 465 SER R 13 REMARK 465 SER R 14 REMARK 465 GLY R 15 REMARK 465 LEU R 16 REMARK 465 VAL R 17 REMARK 465 PRO R 18 REMARK 465 ARG R 19 REMARK 465 GLY R 20 REMARK 465 SER R 21 REMARK 465 HIS R 22 REMARK 465 MET R 23 REMARK 465 HIS R 24 REMARK 465 MET R 25 REMARK 465 GLN R 26 REMARK 465 VAL R 27 REMARK 465 THR R 28 REMARK 465 LEU R 29 REMARK 465 GLN R 30 REMARK 465 VAL R 31 REMARK 465 THR R 32 REMARK 465 PRO R 33 REMARK 465 THR R 200 REMARK 465 LEU R 201 REMARK 465 ARG R 202 REMARK 465 ARG R 203 REMARK 465 PRO R 204 REMARK 465 PRO R 205 REMARK 465 LYS R 206 REMARK 465 GLU R 207 REMARK 465 ALA R 208 REMARK 465 GLN R 209 REMARK 465 ALA R 210 REMARK 465 LEU R 211 REMARK 465 GLU R 212 REMARK 465 HIS R 213 REMARK 465 HIS R 214 REMARK 465 HIS R 215 REMARK 465 HIS R 216 REMARK 465 HIS R 217 REMARK 465 HIS R 218 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 A 173 32.10 -147.27 REMARK 500 ASP A 189 -47.28 -132.03 REMARK 500 ASN A 197 19.19 55.53 REMARK 500 PRO A 231 -105.46 -22.68 REMARK 500 ASP A 233 48.12 -106.22 REMARK 500 LYS A 247 -75.56 -61.06 REMARK 500 HIS R 43 -83.27 -139.08 REMARK 500 LEU R 44 58.75 -104.08 REMARK 500 THR R 188 -164.86 -116.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 233 TYR A 234 149.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA R 1 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS R 134 O REMARK 620 2 ALA R 135 O 66.2 REMARK 620 3 PHE R 138 O 109.1 67.6 REMARK 620 4 SER R 161 OG 159.8 102.3 79.4 REMARK 620 5 VAL R 163 O 74.1 88.7 150.5 89.5 REMARK 620 6 HOH R 239 O 84.9 134.6 92.1 113.6 117.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA R 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL R 219 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ME4 RELATED DB: PDB DBREF 3ME2 A 158 316 UNP O35235 TNF11_MOUSE 158 316 DBREF 3ME2 R 26 210 UNP O35305 TNR11_MOUSE 26 210 SEQADV 3ME2 GLY A 146 UNP O35235 EXPRESSION TAG SEQADV 3ME2 PRO A 147 UNP O35235 EXPRESSION TAG SEQADV 3ME2 LEU A 148 UNP O35235 EXPRESSION TAG SEQADV 3ME2 GLY A 149 UNP O35235 EXPRESSION TAG SEQADV 3ME2 SER A 150 UNP O35235 EXPRESSION TAG SEQADV 3ME2 PRO A 151 UNP O35235 EXPRESSION TAG SEQADV 3ME2 GLU A 152 UNP O35235 EXPRESSION TAG SEQADV 3ME2 PHE A 153 UNP O35235 EXPRESSION TAG SEQADV 3ME2 PRO A 154 UNP O35235 EXPRESSION TAG SEQADV 3ME2 GLY A 155 UNP O35235 EXPRESSION TAG SEQADV 3ME2 ARG A 156 UNP O35235 EXPRESSION TAG SEQADV 3ME2 ARG A 157 UNP O35235 EXPRESSION TAG SEQADV 3ME2 MET R 3 UNP O35305 EXPRESSION TAG SEQADV 3ME2 GLY R 4 UNP O35305 EXPRESSION TAG SEQADV 3ME2 SER R 5 UNP O35305 EXPRESSION TAG SEQADV 3ME2 SER R 6 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 7 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 8 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 9 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 10 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 11 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 12 UNP O35305 EXPRESSION TAG SEQADV 3ME2 SER R 13 UNP O35305 EXPRESSION TAG SEQADV 3ME2 SER R 14 UNP O35305 EXPRESSION TAG SEQADV 3ME2 GLY R 15 UNP O35305 EXPRESSION TAG SEQADV 3ME2 LEU R 16 UNP O35305 EXPRESSION TAG SEQADV 3ME2 VAL R 17 UNP O35305 EXPRESSION TAG SEQADV 3ME2 PRO R 18 UNP O35305 EXPRESSION TAG SEQADV 3ME2 ARG R 19 UNP O35305 EXPRESSION TAG SEQADV 3ME2 GLY R 20 UNP O35305 EXPRESSION TAG SEQADV 3ME2 SER R 21 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 22 UNP O35305 EXPRESSION TAG SEQADV 3ME2 MET R 23 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 24 UNP O35305 EXPRESSION TAG SEQADV 3ME2 MET R 25 UNP O35305 EXPRESSION TAG SEQADV 3ME2 LEU R 211 UNP O35305 EXPRESSION TAG SEQADV 3ME2 GLU R 212 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 213 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 214 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 215 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 216 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 217 UNP O35305 EXPRESSION TAG SEQADV 3ME2 HIS R 218 UNP O35305 EXPRESSION TAG SEQRES 1 A 171 GLY PRO LEU GLY SER PRO GLU PHE PRO GLY ARG ARG LYS SEQRES 2 A 171 PRO GLU ALA GLN PRO PHE ALA HIS LEU THR ILE ASN ALA SEQRES 3 A 171 ALA SER ILE PRO SER GLY SER HIS LYS VAL THR LEU SER SEQRES 4 A 171 SER TRP TYR HIS ASP ARG GLY TRP ALA LYS ILE SER ASN SEQRES 5 A 171 MET THR LEU SER ASN GLY LYS LEU ARG VAL ASN GLN ASP SEQRES 6 A 171 GLY PHE TYR TYR LEU TYR ALA ASN ILE CYS PHE ARG HIS SEQRES 7 A 171 HIS GLU THR SER GLY SER VAL PRO THR ASP TYR LEU GLN SEQRES 8 A 171 LEU MET VAL TYR VAL VAL LYS THR SER ILE LYS ILE PRO SEQRES 9 A 171 SER SER HIS ASN LEU MET LYS GLY GLY SER THR LYS ASN SEQRES 10 A 171 TRP SER GLY ASN SER GLU PHE HIS PHE TYR SER ILE ASN SEQRES 11 A 171 VAL GLY GLY PHE PHE LYS LEU ARG ALA GLY GLU GLU ILE SEQRES 12 A 171 SER ILE GLN VAL SER ASN PRO SER LEU LEU ASP PRO ASP SEQRES 13 A 171 GLN ASP ALA THR TYR PHE GLY ALA PHE LYS VAL GLN ASP SEQRES 14 A 171 ILE ASP SEQRES 1 R 216 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 R 216 LEU VAL PRO ARG GLY SER HIS MET HIS MET GLN VAL THR SEQRES 3 R 216 LEU GLN VAL THR PRO PRO CYS THR GLN GLU ARG HIS TYR SEQRES 4 R 216 GLU HIS LEU GLY ARG CYS CYS SER ARG CYS GLU PRO GLY SEQRES 5 R 216 LYS TYR LEU SER SER LYS CYS THR PRO THR SER ASP SER SEQRES 6 R 216 VAL CYS LEU PRO CYS GLY PRO ASP GLU TYR LEU ASP THR SEQRES 7 R 216 TRP ASN GLU GLU ASP LYS CYS LEU LEU HIS LYS VAL CYS SEQRES 8 R 216 ASP ALA GLY LYS ALA LEU VAL ALA VAL ASP PRO GLY ASN SEQRES 9 R 216 HIS THR ALA PRO ARG ARG CYS ALA CYS THR ALA GLY TYR SEQRES 10 R 216 HIS TRP ASN SER ASP CYS GLU CYS CYS ARG ARG ASN THR SEQRES 11 R 216 GLU CYS ALA PRO GLY PHE GLY ALA GLN HIS PRO LEU GLN SEQRES 12 R 216 LEU ASN LYS ASP THR VAL CYS THR PRO CYS LEU LEU GLY SEQRES 13 R 216 PHE PHE SER ASP VAL PHE SER SER THR ASP LYS CYS LYS SEQRES 14 R 216 PRO TRP THR ASN CYS THR LEU LEU GLY LYS LEU GLU ALA SEQRES 15 R 216 HIS GLN GLY THR THR GLU SER ASP VAL VAL CYS SER SER SEQRES 16 R 216 SER MET THR LEU ARG ARG PRO PRO LYS GLU ALA GLN ALA SEQRES 17 R 216 LEU GLU HIS HIS HIS HIS HIS HIS HET CL A 5 1 HET CL A 6 1 HET CL A 7 1 HET NA R 1 1 HET CL R 219 1 HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 3 CL 4(CL 1-) FORMUL 6 NA NA 1+ FORMUL 8 HOH *45(H2 O) HELIX 1 1 ALA A 171 ILE A 174 5 4 HELIX 2 2 THR A 226 GLY A 228 5 3 HELIX 3 3 ASN A 294 LEU A 298 5 5 HELIX 4 4 ASP R 94 LYS R 97 5 4 HELIX 5 5 ASN R 175 GLY R 180 5 6 SHEET 1 A 3 TRP A 186 TYR A 187 0 SHEET 2 A 3 PHE A 164 ILE A 169 -1 N THR A 168 O TYR A 187 SHEET 3 A 3 LYS A 194 SER A 196 -1 O LYS A 194 N HIS A 166 SHEET 1 B 5 TRP A 186 TYR A 187 0 SHEET 2 B 5 PHE A 164 ILE A 169 -1 N THR A 168 O TYR A 187 SHEET 3 B 5 TYR A 306 GLN A 313 -1 O PHE A 307 N LEU A 167 SHEET 4 B 5 GLY A 211 HIS A 224 -1 N PHE A 212 O VAL A 312 SHEET 5 B 5 PHE A 269 LEU A 282 -1 O TYR A 272 N PHE A 221 SHEET 1 C 4 VAL A 181 THR A 182 0 SHEET 2 C 4 GLU A 286 VAL A 292 -1 O VAL A 292 N VAL A 181 SHEET 3 C 4 LYS A 204 VAL A 207 -1 N LEU A 205 O ILE A 288 SHEET 4 C 4 MET A 198 SER A 201 -1 N THR A 199 O ARG A 206 SHEET 1 D 4 VAL A 181 THR A 182 0 SHEET 2 D 4 GLU A 286 VAL A 292 -1 O VAL A 292 N VAL A 181 SHEET 3 D 4 LEU A 235 SER A 245 -1 N VAL A 242 O SER A 289 SHEET 4 D 4 HIS A 252 LYS A 261 -1 O LEU A 254 N VAL A 241 SHEET 1 E 2 HIS R 40 GLU R 42 0 SHEET 2 E 2 CYS R 47 SER R 49 -1 O CYS R 48 N TYR R 41 SHEET 1 F 2 LYS R 55 SER R 59 0 SHEET 2 F 2 VAL R 68 PRO R 71 -1 O LEU R 70 N TYR R 56 SHEET 1 G 2 GLU R 76 TYR R 77 0 SHEET 2 G 2 LEU R 88 LEU R 89 -1 O LEU R 88 N TYR R 77 SHEET 1 H 2 LEU R 99 ASP R 103 0 SHEET 2 H 2 ARG R 112 CYS R 115 -1 O ARG R 112 N ASP R 103 SHEET 1 I 2 TYR R 119 ASN R 122 0 SHEET 2 I 2 CYS R 127 ARG R 130 -1 O ARG R 129 N HIS R 120 SHEET 1 J 2 PHE R 138 ALA R 140 0 SHEET 2 J 2 CYS R 152 PRO R 154 -1 O THR R 153 N GLY R 139 SHEET 1 K 2 PHE R 159 PHE R 160 0 SHEET 2 K 2 LYS R 171 PRO R 172 -1 O LYS R 171 N PHE R 160 SHEET 1 L 2 LEU R 182 HIS R 185 0 SHEET 2 L 2 VAL R 194 SER R 196 -1 O SER R 196 N LEU R 182 SSBOND 1 CYS R 35 CYS R 47 1555 1555 2.04 SSBOND 2 CYS R 48 CYS R 61 1555 1555 2.03 SSBOND 3 CYS R 51 CYS R 69 1555 1555 2.04 SSBOND 4 CYS R 72 CYS R 87 1555 1555 2.06 SSBOND 5 CYS R 93 CYS R 113 1555 1555 2.05 SSBOND 6 CYS R 115 CYS R 128 1555 1555 2.04 SSBOND 7 CYS R 125 CYS R 127 1555 1555 2.07 SSBOND 8 CYS R 134 CYS R 152 1555 1555 2.06 SSBOND 9 CYS R 155 CYS R 170 1555 1555 2.05 SSBOND 10 CYS R 176 CYS R 195 1555 1555 2.05 LINK NA NA R 1 O CYS R 134 1555 1555 2.74 LINK NA NA R 1 O ALA R 135 1555 1555 2.97 LINK NA NA R 1 O PHE R 138 1555 1555 2.42 LINK NA NA R 1 OG SER R 161 1555 1555 2.49 LINK NA NA R 1 O VAL R 163 1555 1555 2.62 LINK NA NA R 1 O HOH R 239 1555 1555 2.71 CISPEP 1 HIS R 142 PRO R 143 0 -3.14 SITE 1 AC1 6 SER A 184 SER A 185 TRP A 186 LEU A 200 SITE 2 AC1 6 ASN A 202 GLY A 203 SITE 1 AC2 3 HIS A 188 ASP A 189 ARG A 190 SITE 1 AC3 3 LYS A 194 LYS A 281 LYS R 86 SITE 1 AC4 6 CYS R 134 ALA R 135 PHE R 138 SER R 161 SITE 2 AC4 6 VAL R 163 HOH R 239 SITE 1 AC5 3 HIS R 90 LYS R 91 ARG R 111 CRYST1 121.225 121.225 94.995 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 0.008249 0.004763 0.000000 0.00000 SCALE2 0.000000 0.009525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010527 0.00000