HEADER CYTOKINE 26-MAY-15 5BNQ TITLE CRYSTAL STRUCTURE OF HRANKL-MRANK COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OSTEOCLAST DIFFERENTIATION FACTOR,ODF,OSTEOPROTEGERIN COMPND 5 LIGAND,OPGL,RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA-B LIGAND, COMPND 6 RANKL,TNF-RELATED ACTIVATION-INDUCED CYTOKINE,TRANCE; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11A; COMPND 10 CHAIN: R; COMPND 11 SYNONYM: OSTEOCLAST DIFFERENTIATION FACTOR RECEPTOR,ODFR,RECEPTOR COMPND 12 ACTIVATOR OF NF-KB, RANK; COMPND 13 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: TNFSF11, OPGL, RANKL, TRANCE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PLASMID; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 14 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 GENE: TNFRSF11A, RANK; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 20 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PLASMID KEYWDS RANK, RANKL, RANKL-RANK COMPLEX, TNFSF11, TNFRSF11A, TNF SUPERFAMILY, KEYWDS 2 CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR J.REN REVDAT 2 10-JAN-24 5BNQ 1 REMARK REVDAT 1 14-OCT-15 5BNQ 0 JRNL AUTH C.LIU,Y.ZHAO,W.HE,W.WANG,Y.CHEN,S.ZHANG,Y.MA,J.GOHDA, JRNL AUTH 2 T.ISHIDA,T.S.WALTER,R.J.OWENS,D.I.STUART,J.REN,B.GAO JRNL TITL A RANKL MUTANT USED AS AN INTER-SPECIES VACCINE FOR JRNL TITL 2 EFFICIENT IMMUNOTHERAPY OF OSTEOPOROSIS. JRNL REF SCI REP V. 5 14150 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 26412210 JRNL DOI 10.1038/SREP14150 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 29.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18885 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1018 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) : 2.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1311 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2505 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -1.15000 REMARK 3 B12 (A**2) : 0.35000 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): 0.271 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.775 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2598 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3533 ; 1.303 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 5.759 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;34.218 ;24.052 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 410 ;14.765 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.403 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 374 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1973 ; 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): 1286 ; 3.081 ; 8.526 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1604 ; 4.859 ;14.354 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1312 ; 4.748 ; 9.296 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3744 ; 8.874 ;32.067 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 : 3 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 162 A 316 REMARK 3 ORIGIN FOR THE GROUP (A): 59.5130 48.0500 46.8670 REMARK 3 T TENSOR REMARK 3 T11: 0.2108 T22: 0.1845 REMARK 3 T33: 0.0513 T12: -0.0011 REMARK 3 T13: 0.0368 T23: -0.0132 REMARK 3 L TENSOR REMARK 3 L11: 1.4887 L22: 1.0898 REMARK 3 L33: 0.9321 L12: -0.2952 REMARK 3 L13: -0.0254 L23: -0.2668 REMARK 3 S TENSOR REMARK 3 S11: 0.0998 S12: -0.0632 S13: 0.2494 REMARK 3 S21: 0.0810 S22: -0.0060 S23: -0.0397 REMARK 3 S31: -0.2900 S32: -0.0344 S33: -0.0938 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 114 REMARK 3 ORIGIN FOR THE GROUP (A): 83.7860 55.1340 57.5860 REMARK 3 T TENSOR REMARK 3 T11: 0.2613 T22: 0.4419 REMARK 3 T33: 0.2442 T12: -0.1456 REMARK 3 T13: 0.0015 T23: -0.2141 REMARK 3 L TENSOR REMARK 3 L11: 2.8961 L22: 1.2067 REMARK 3 L33: 9.9359 L12: 0.8868 REMARK 3 L13: 0.8611 L23: 2.5870 REMARK 3 S TENSOR REMARK 3 S11: 0.1008 S12: -0.5489 S13: 0.6764 REMARK 3 S21: -0.0266 S22: 0.1396 S23: -0.0495 REMARK 3 S31: -0.3956 S32: -0.0108 S33: -0.2404 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 115 R 199 REMARK 3 ORIGIN FOR THE GROUP (A): 81.0900 59.6750 10.6190 REMARK 3 T TENSOR REMARK 3 T11: 0.2476 T22: 0.3600 REMARK 3 T33: 0.0821 T12: -0.0918 REMARK 3 T13: 0.0495 T23: 0.0448 REMARK 3 L TENSOR REMARK 3 L11: 1.7962 L22: 1.2947 REMARK 3 L33: 5.2153 L12: 1.1450 REMARK 3 L13: -2.2876 L23: -2.3243 REMARK 3 S TENSOR REMARK 3 S11: 0.1980 S12: 0.2862 S13: 0.2829 REMARK 3 S21: 0.1229 S22: 0.0578 S23: 0.1961 REMARK 3 S31: -0.3224 S32: -0.3871 S33: -0.2557 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5BNQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000210246. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87260 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19916 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.19700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.81800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 3ME2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM DI-HYDROGEN PHOSPHATE, 2 REMARK 280 M SODIUM CHLORIDE, 0.1 M POTASSIUM DI-HYDROGEN PHOSPHATE AND 0.1 REMARK 280 M MES, 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 47.23650 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 47.23650 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 47.23650 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: 19810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -356.0 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 122.18800 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 61.09400 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 105.81791 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL A 402 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 525 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 542 LIES ON A SPECIAL POSITION. 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 SER A 158 REMARK 465 LYS A 159 REMARK 465 LEU A 160 REMARK 465 GLU A 161 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 GLN A 163 76.28 59.74 REMARK 500 ASP A 174 41.55 -148.08 REMARK 500 ASP A 190 54.60 -150.47 REMARK 500 LYS A 248 -74.32 -78.53 REMARK 500 ARG R 39 -14.27 70.89 REMARK 500 ASP R 94 109.32 -58.36 REMARK 500 THR R 188 -163.78 -118.34 REMARK 500 VAL R 193 153.95 -45.69 REMARK 500 SER R 198 -160.36 -75.38 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 304 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS R 134 O REMARK 620 2 ALA R 135 O 63.3 REMARK 620 3 PHE R 138 O 105.9 63.5 REMARK 620 4 SER R 161 OG 157.6 100.2 76.8 REMARK 620 5 VAL R 163 O 71.9 77.6 135.5 90.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 R 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 R 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 R 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA R 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL R 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL R 306 DBREF 5BNQ A 158 317 UNP O14788 TNF11_HUMAN 158 317 DBREF 5BNQ R 26 210 UNP O35305 TNR11_MOUSE 26 210 SEQADV 5BNQ MET R 3 UNP O35305 INITIATING METHIONINE SEQADV 5BNQ GLY R 4 UNP O35305 EXPRESSION TAG SEQADV 5BNQ SER R 5 UNP O35305 EXPRESSION TAG SEQADV 5BNQ SER R 6 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 7 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 8 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 9 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 10 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 11 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 12 UNP O35305 EXPRESSION TAG SEQADV 5BNQ SER R 13 UNP O35305 EXPRESSION TAG SEQADV 5BNQ SER R 14 UNP O35305 EXPRESSION TAG SEQADV 5BNQ GLY R 15 UNP O35305 EXPRESSION TAG SEQADV 5BNQ LEU R 16 UNP O35305 EXPRESSION TAG SEQADV 5BNQ VAL R 17 UNP O35305 EXPRESSION TAG SEQADV 5BNQ PRO R 18 UNP O35305 EXPRESSION TAG SEQADV 5BNQ ARG R 19 UNP O35305 EXPRESSION TAG SEQADV 5BNQ GLY R 20 UNP O35305 EXPRESSION TAG SEQADV 5BNQ SER R 21 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 22 UNP O35305 EXPRESSION TAG SEQADV 5BNQ MET R 23 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 24 UNP O35305 EXPRESSION TAG SEQADV 5BNQ MET R 25 UNP O35305 EXPRESSION TAG SEQADV 5BNQ LEU R 211 UNP O35305 EXPRESSION TAG SEQADV 5BNQ GLU R 212 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 213 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 214 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 215 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 216 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 217 UNP O35305 EXPRESSION TAG SEQADV 5BNQ HIS R 218 UNP O35305 EXPRESSION TAG SEQRES 1 A 160 SER LYS LEU GLU ALA GLN PRO PHE ALA HIS LEU THR ILE SEQRES 2 A 160 ASN ALA THR ASP ILE PRO SER GLY SER HIS LYS VAL SER SEQRES 3 A 160 LEU SER SER TRP TYR HIS ASP ARG GLY TRP ALA LYS ILE SEQRES 4 A 160 SER ASN MET THR PHE SER ASN GLY LYS LEU ILE VAL ASN SEQRES 5 A 160 GLN ASP GLY PHE TYR TYR LEU TYR ALA ASN ILE CYS PHE SEQRES 6 A 160 ARG HIS HIS GLU THR SER GLY ASP LEU ALA THR GLU TYR SEQRES 7 A 160 LEU GLN LEU MET VAL TYR VAL THR LYS THR SER ILE LYS SEQRES 8 A 160 ILE PRO SER SER HIS THR LEU MET LYS GLY GLY SER THR SEQRES 9 A 160 LYS TYR TRP SER GLY ASN SER GLU PHE HIS PHE TYR SER SEQRES 10 A 160 ILE ASN VAL GLY GLY PHE PHE LYS LEU ARG SER GLY GLU SEQRES 11 A 160 GLU ILE SER ILE GLU VAL SER ASN PRO SER LEU LEU ASP SEQRES 12 A 160 PRO ASP GLN ASP ALA THR TYR PHE GLY ALA PHE LYS VAL SEQRES 13 A 160 ARG ASP 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 PO4 A 401 5 HET CL A 402 1 HET CL A 403 1 HET CL A 404 1 HET CL A 405 1 HET CL A 406 1 HET PO4 R 301 5 HET PO4 R 302 5 HET PO4 R 303 5 HET NA R 304 1 HET CL R 305 1 HET CL R 306 1 HET CL R 307 1 HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 3 PO4 4(O4 P 3-) FORMUL 4 CL 8(CL 1-) FORMUL 12 NA NA 1+ FORMUL 16 HOH *79(H2 O) HELIX 1 AA1 ALA A 172 ILE A 175 5 4 HELIX 2 AA2 THR A 227 GLY A 229 5 3 HELIX 3 AA3 ASN A 295 LEU A 299 5 5 HELIX 4 AA4 ASP R 94 LYS R 97 5 4 HELIX 5 AA5 ASN R 175 GLY R 180 5 6 SHEET 1 AA1 3 TRP A 187 TYR A 188 0 SHEET 2 AA1 3 PHE A 165 ILE A 170 -1 N THR A 169 O TYR A 188 SHEET 3 AA1 3 LYS A 195 SER A 197 -1 O LYS A 195 N HIS A 167 SHEET 1 AA2 5 TRP A 187 TYR A 188 0 SHEET 2 AA2 5 PHE A 165 ILE A 170 -1 N THR A 169 O TYR A 188 SHEET 3 AA2 5 TYR A 307 ARG A 314 -1 O PHE A 308 N LEU A 168 SHEET 4 AA2 5 GLY A 212 HIS A 225 -1 N PHE A 213 O VAL A 313 SHEET 5 AA2 5 PHE A 270 LEU A 283 -1 O TYR A 273 N PHE A 222 SHEET 1 AA3 4 VAL A 182 LEU A 184 0 SHEET 2 AA3 4 GLU A 287 VAL A 293 -1 O ILE A 291 N LEU A 184 SHEET 3 AA3 4 LYS A 205 VAL A 208 -1 N VAL A 208 O GLU A 287 SHEET 4 AA3 4 MET A 199 SER A 202 -1 N THR A 200 O ILE A 207 SHEET 1 AA4 4 VAL A 182 LEU A 184 0 SHEET 2 AA4 4 GLU A 287 VAL A 293 -1 O ILE A 291 N LEU A 184 SHEET 3 AA4 4 TYR A 235 SER A 246 -1 N THR A 245 O GLU A 288 SHEET 4 AA4 4 HIS A 253 TYR A 263 -1 O LEU A 255 N VAL A 242 SHEET 1 AA5 2 HIS R 40 HIS R 43 0 SHEET 2 AA5 2 ARG R 46 SER R 49 -1 O CYS R 48 N TYR R 41 SHEET 1 AA6 2 LYS R 55 SER R 59 0 SHEET 2 AA6 2 VAL R 68 PRO R 71 -1 O LEU R 70 N TYR R 56 SHEET 1 AA7 2 GLU R 76 TYR R 77 0 SHEET 2 AA7 2 LEU R 88 LEU R 89 -1 O LEU R 88 N TYR R 77 SHEET 1 AA8 2 LEU R 99 ASP R 103 0 SHEET 2 AA8 2 ARG R 112 CYS R 115 -1 O ARG R 112 N ASP R 103 SHEET 1 AA9 2 TYR R 119 ASN R 122 0 SHEET 2 AA9 2 CYS R 127 ARG R 130 -1 O ARG R 129 N HIS R 120 SHEET 1 AB1 2 PHE R 138 ALA R 140 0 SHEET 2 AB1 2 CYS R 152 PRO R 154 -1 O THR R 153 N GLY R 139 SHEET 1 AB2 2 PHE R 159 PHE R 160 0 SHEET 2 AB2 2 LYS R 171 PRO R 172 -1 O LYS R 171 N PHE R 160 SHEET 1 AB3 2 LEU R 182 HIS R 185 0 SHEET 2 AB3 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 2.02 SSBOND 3 CYS R 51 CYS R 69 1555 1555 2.04 SSBOND 4 CYS R 72 CYS R 87 1555 1555 2.05 SSBOND 5 CYS R 93 CYS R 113 1555 1555 2.04 SSBOND 6 CYS R 115 CYS R 128 1555 1555 2.04 SSBOND 7 CYS R 125 CYS R 127 1555 1555 2.06 SSBOND 8 CYS R 134 CYS R 152 1555 1555 2.05 SSBOND 9 CYS R 155 CYS R 170 1555 1555 2.03 SSBOND 10 CYS R 176 CYS R 195 1555 1555 2.04 LINK O CYS R 134 NA NA R 304 1555 1555 2.88 LINK O ALA R 135 NA NA R 304 1555 1555 2.93 LINK O PHE R 138 NA NA R 304 1555 1555 2.50 LINK OG SER R 161 NA NA R 304 1555 1555 2.71 LINK O VAL R 163 NA NA R 304 1555 1555 2.59 CISPEP 1 HIS R 142 PRO R 143 0 -1.97 SITE 1 AC1 2 GLN A 163 VAL A 313 SITE 1 AC2 1 LYS A 262 SITE 1 AC3 3 THR A 261 TRP A 264 HIS A 271 SITE 1 AC4 3 LYS A 195 LYS A 282 LYS R 86 SITE 1 AC5 3 HIS A 189 ASP A 190 ARG A 191 SITE 1 AC6 8 GLN A 237 MET A 239 LYS A 257 PHE A 272 SITE 2 AC6 8 ASP A 300 LYS R 97 CYS R 125 GLU R 126 SITE 1 AC7 4 CYS R 113 TRP R 121 ASN R 147 HOH R 401 SITE 1 AC8 5 ALA R 117 GLY R 118 ASN R 131 LEU R 144 SITE 2 AC8 5 GLN R 145 SITE 1 AC9 5 CYS R 134 ALA R 135 PHE R 138 SER R 161 SITE 2 AC9 5 VAL R 163 SITE 1 AD1 4 HIS R 90 LYS R 91 PRO R 110 ARG R 111 SITE 1 AD2 2 HIS R 120 ASN R 122 CRYST1 122.188 122.188 94.473 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 0.008184 0.004725 0.000000 0.00000 SCALE2 0.000000 0.009450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010585 0.00000