HEADER CYTOKINE, HORMONE/GROWTH FACTOR 28-JUL-04 1U5X TITLE CRYSTAL STRUCTURE OF MURINE APRIL AT PH 5.0 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, JELLY-ROLL, TRIMER, HORMONE-GROWTH FACTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.J.WALLWEBER,D.M.COMPAAN,M.A.STAROVASNIK,S.G.HYMOWITZ REVDAT 3 13-JUL-11 1U5X 1 VERSN REVDAT 2 24-FEB-09 1U5X 1 VERSN REVDAT 1 12-OCT-04 1U5X 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.07 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11697 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1136 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 627 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.4580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 994 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 30.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.64 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): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.704 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1025 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 968 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1391 ; 1.511 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2222 ; 0.828 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 127 ; 6.739 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ;27.584 ;21.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 163 ;15.216 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;24.941 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 163 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1129 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 223 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 149 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1056 ; 0.257 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 619 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 34 ; 0.162 ; 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): 17 ; 0.231 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 74 ; 0.302 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.211 ; 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): 643 ; 2.570 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1034 ; 3.604 ; 6.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 382 ; 3.852 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 357 ; 5.559 ; 8.000 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): 17.4225 13.7804 59.4666 REMARK 3 T TENSOR REMARK 3 T11: 0.1164 T22: 0.0259 REMARK 3 T33: 0.0609 T12: 0.0033 REMARK 3 T13: -0.0532 T23: -0.0322 REMARK 3 L TENSOR REMARK 3 L11: 4.2488 L22: 2.5135 REMARK 3 L33: 4.9307 L12: -0.5897 REMARK 3 L13: -0.5612 L23: 0.3975 REMARK 3 S TENSOR REMARK 3 S11: -0.0373 S12: 0.2567 S13: -0.3726 REMARK 3 S21: -0.3268 S22: -0.0324 S23: 0.3005 REMARK 3 S31: 0.5213 S32: -0.0681 S33: 0.0697 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1U5X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-04. REMARK 100 THE RCSB ID CODE IS RCSB023285. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11701 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04200 REMARK 200 FOR THE DATA SET : 30.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44200 REMARK 200 FOR SHELL : 5.000 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: APRIL AT PH 8.5 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 CITRIC ACID, 1.0 M LICL, PH 5.0, REMARK 280 VAPOR 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 45.38950 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 45.38950 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 45.38950 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 45.38950 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 45.38950 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 45.38950 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 45.38950 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 45.38950 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 45.38950 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 45.38950 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 45.38950 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 45.38950 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 45.38950 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 45.38950 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 45.38950 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 45.38950 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 45.38950 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 45.38950 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 45.38950 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 45.38950 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 45.38950 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 45.38950 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 45.38950 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 45.38950 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 45.38950 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 45.38950 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 45.38950 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 FORMED BY THE 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: 4930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 90.77900 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 90.77900 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 90.77900 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 90.77900 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 ASP A 121 REMARK 465 SER A 122 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 LYS A 105 CG CD CE NZ REMARK 470 SER A 118 OG REMARK 470 ASP A 123 CG OD1 OD2 REMARK 470 HIS A 163 CG ND1 CD2 CE1 NE2 REMARK 470 PHE A 167 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 178 CG CD OE1 NE2 REMARK 470 ARG A 180 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 194 CG OD1 OD2 REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 226 CD CE NZ 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 OD2 ASP A 150 O HOH A 17 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 164 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES 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 20.74 -140.26 REMARK 500 THR A 166 -65.92 73.65 REMARK 500 GLN A 178 88.56 -50.82 REMARK 500 PRO A 221 48.48 -78.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U5Y RELATED DB: PDB REMARK 900 SAME PROTEIN CRYSTALLZED IN C2 SPACE GROUP AT PH 8.0 REMARK 900 RELATED ID: 1U5Z RELATED DB: PDB REMARK 900 SAME PROTEIN CRYSTALLZED IN I23 SPACE GROUP AT PH 8.5 DBREF 1U5X A 104 241 UNP Q9D777 TNF13_MOUSE 104 241 SEQADV 1U5X GLY A 102 UNP Q9D777 CLONING ARTIFACT SEQADV 1U5X 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 FORMUL 2 HOH *43(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 VAL A 172 GLU A 176 -1 N VAL A 172 O LYS A 219 SHEET 5 A 5 ARG A 181 ARG A 186 -1 O LEU A 184 N VAL A 173 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 HIS A 110 O VAL A 132 SHEET 6 B 8 PHE A 235 LYS A 240 -1 O LEU A 236 N LEU A 111 SHEET 7 B 8 GLY A 152 PHE A 162 -1 N TYR A 157 O GLY A 237 SHEET 8 B 8 ASN A 200 LEU A 210 -1 O LEU A 210 N GLY A 152 SSBOND 1 CYS A 187 CYS A 202 1555 1555 2.02 CRYST1 90.779 90.779 90.779 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 0.011016 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011016 0.00000