HEADER CYTOKINE, HORMONE/GROWTH FACTOR 28-JUL-04 1U5Z TITLE THE CRYSTAL STRUCTURE OF MURINE APRIL, PH 8.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TNF DOMAIN OF MURINE APRIL; COMPND 5 SYNONYM: A PROLIFERATION- INDUCING LIGAND, APRIL; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TNFSF13, APRIL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-32A (MODIFIED) KEYWDS TNFSF, CYTOKINE, TRIMER, JELLY-ROLL, HORMONE-GROWTH FACTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.J.WALLWEBER,D.M.COMPAAN,M.A.STAROVASNIK,S.G.HYMOWITZ REVDAT 4 23-AUG-23 1U5Z 1 REMARK SEQADV REVDAT 3 13-JUL-11 1U5Z 1 VERSN REVDAT 2 24-FEB-09 1U5Z 1 VERSN REVDAT 1 12-OCT-04 1U5Z 0 JRNL AUTH H.J.WALLWEBER,D.M.COMPAAN,M.A.STAROVASNIK,S.G.HYMOWITZ JRNL TITL THE CRYSTAL STRUCTURE OF A PROLIFERATION-INDUCING LIGAND, JRNL TITL 2 APRIL. JRNL REF J.MOL.BIOL. V. 343 283 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15451660 JRNL DOI 10.1016/J.JMB.2004.08.040 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.07 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5231 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 506 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 266 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 988 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 60.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.34 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.654 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.303 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.216 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.034 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1009 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 938 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1367 ; 1.157 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2160 ; 0.706 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 125 ; 6.629 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ;28.824 ;22.143 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 162 ;17.162 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;14.361 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 158 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1114 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 216 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 151 ; 0.186 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1021 ; 0.234 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 614 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 16 ; 0.288 ; 0.200 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): 13 ; 0.296 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 58 ; 0.243 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.118 ; 0.200 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): 631 ; 1.801 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1010 ; 2.760 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 378 ; 2.418 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 357 ; 3.746 ; 8.000 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 : 1 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 105 A 241 REMARK 3 ORIGIN FOR THE GROUP (A): 78.8600 61.1840 64.1250 REMARK 3 T TENSOR REMARK 3 T11: 0.0971 T22: 0.0705 REMARK 3 T33: 0.2085 T12: 0.0483 REMARK 3 T13: 0.0504 T23: -0.0670 REMARK 3 L TENSOR REMARK 3 L11: 7.4656 L22: 4.2619 REMARK 3 L33: 7.5870 L12: -0.6856 REMARK 3 L13: 0.8217 L23: -1.0219 REMARK 3 S TENSOR REMARK 3 S11: 0.0921 S12: 0.3582 S13: -0.8896 REMARK 3 S21: -0.3802 S22: 0.0747 S23: -0.4547 REMARK 3 S31: 0.6784 S32: 0.6350 S33: -0.1668 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U5Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTALS SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5238 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.46100 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: TRUNCATED MODEL OF BAFF (PDB ENTRY 1OSG) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.5, 0.5 M KSCN, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 46.08300 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 46.08300 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 46.08300 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 46.08300 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 46.08300 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 46.08300 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 46.08300 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 46.08300 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 46.08300 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 46.08300 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 46.08300 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 46.08300 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 46.08300 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 46.08300 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 46.08300 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 46.08300 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 46.08300 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 46.08300 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 46.08300 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 46.08300 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 46.08300 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 46.08300 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 46.08300 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 46.08300 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 46.08300 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 46.08300 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 300 REMARK: THE BIOLOGICALLY RELEVANT TRIMER IS GENERATED BY A REMARK 300 CRYSTALLOGRAPHIC 3-FOLD 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 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 102 REMARK 465 SER A 103 REMARK 465 LYS A 104 REMARK 465 LYS A 119 REMARK 465 ALA A 120 REMARK 465 MET A 191 REMARK 465 PRO A 192 REMARK 465 SER A 193 REMARK 465 ASP A 194 REMARK 465 PRO A 195 REMARK 465 ASP A 196 REMARK 465 ARG A 197 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 ASN A 115 CG OD1 ND2 REMARK 470 ASP A 121 CG OD1 OD2 REMARK 470 SER A 122 OG REMARK 470 VAL A 165 CG1 CG2 REMARK 470 PHE A 167 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR A 168 OG1 CG2 REMARK 470 ARG A 189 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 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 OG SER A 158 OE1 GLN A 171 1.97 REMARK 500 NH1 ARG A 135 O HOH A 9 2.13 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 ARG A 137 37.34 -165.33 REMARK 500 PRO A 221 4.19 -68.82 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 NI A 101 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 106 NE2 REMARK 620 2 HIS A 106 NE2 73.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U5X RELATED DB: PDB REMARK 900 SAME PROTEIN RYSTALLIZED IN SPACE GROUP I23 AT PH 5.0 REMARK 900 RELATED ID: 1U5Y RELATED DB: PDB REMARK 900 SAME PROTEIN RYSTALLIZED IN SPACE GROUP C2 AT PH 8.0 DBREF 1U5Z A 104 241 UNP Q9D777 TNF13_MOUSE 104 241 SEQADV 1U5Z GLY A 102 UNP Q9D777 CLONING ARTIFACT SEQADV 1U5Z SER A 103 UNP Q9D777 CLONING ARTIFACT SEQRES 1 A 140 GLY SER LYS LYS HIS SER VAL LEU HIS LEU VAL PRO VAL SEQRES 2 A 140 ASN ILE THR SER LYS ALA ASP SER ASP VAL THR GLU VAL SEQRES 3 A 140 MET TRP GLN PRO VAL LEU ARG ARG GLY ARG GLY LEU GLU SEQRES 4 A 140 ALA GLN GLY ASP ILE VAL ARG VAL TRP ASP THR GLY ILE SEQRES 5 A 140 TYR LEU LEU TYR SER GLN VAL LEU PHE HIS ASP VAL THR SEQRES 6 A 140 PHE THR MET GLY GLN VAL VAL SER ARG GLU GLY GLN GLY SEQRES 7 A 140 ARG ARG GLU THR LEU PHE ARG CYS ILE ARG SER MET PRO SEQRES 8 A 140 SER ASP PRO ASP ARG ALA TYR ASN SER CYS TYR SER ALA SEQRES 9 A 140 GLY VAL PHE HIS LEU HIS GLN GLY ASP ILE ILE THR VAL SEQRES 10 A 140 LYS ILE PRO ARG ALA ASN ALA LYS LEU SER LEU SER PRO SEQRES 11 A 140 HIS GLY THR PHE LEU GLY PHE VAL LYS LEU HET NI A 101 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *18(H2 O) SHEET 1 A 5 LEU A 139 GLN A 142 0 SHEET 2 A 5 ILE A 145 VAL A 148 -1 O ARG A 147 N GLU A 140 SHEET 3 A 5 ILE A 215 ILE A 220 -1 O ILE A 216 N VAL A 146 SHEET 4 A 5 MET A 169 GLU A 176 -1 N VAL A 172 O LYS A 219 SHEET 5 A 5 ARG A 181 ARG A 189 -1 O GLU A 182 N ARG A 175 SHEET 1 B 8 LEU A 139 GLN A 142 0 SHEET 2 B 8 ILE A 145 VAL A 148 -1 O ARG A 147 N GLU A 140 SHEET 3 B 8 ILE A 215 ILE A 220 -1 O ILE A 216 N VAL A 146 SHEET 4 B 8 THR A 125 ARG A 135 -1 N THR A 125 O ILE A 220 SHEET 5 B 8 VAL A 108 THR A 117 -1 N ASN A 115 O MET A 128 SHEET 6 B 8 PHE A 235 LEU A 241 -1 O LEU A 236 N LEU A 111 SHEET 7 B 8 GLY A 152 PHE A 162 -1 N ILE A 153 O LEU A 241 SHEET 8 B 8 ASN A 200 LEU A 210 -1 O ASN A 200 N PHE A 162 SSBOND 1 CYS A 187 CYS A 202 1555 1555 2.05 LINK NI NI A 101 NE2 HIS A 106 1555 9555 2.57 LINK NI NI A 101 NE2 HIS A 106 1555 5555 2.72 SITE 1 AC1 1 HIS A 106 CRYST1 92.166 92.166 92.166 90.00 90.00 90.00 I 2 3 24 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 0.010850 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010850 0.00000