HEADER CYTOKINE, HORMONE/GROWTH FACTOR 28-JUL-04 1U5Y TITLE CRYSTAL STRUCTURE OF MURINE APRIL, PH 8.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13; COMPND 3 CHAIN: A, B, D; 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 TRIMER, JELLY-ROLL, CYTOKINE, TNFSF, HORMONE-GROWTH FACTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.J.WALLWEBER,D.M.COMPAAN,M.A.STAROVASNIK,S.G.HYMOWITZ REVDAT 4 04-APR-18 1U5Y 1 REMARK REVDAT 3 13-JUL-11 1U5Y 1 VERSN REVDAT 2 24-FEB-09 1U5Y 1 VERSN REVDAT 1 12-OCT-04 1U5Y 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. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 20737 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2210 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1081 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3139 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 37.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.34000 REMARK 3 B22 (A**2) : -2.02000 REMARK 3 B33 (A**2) : 0.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.92000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.369 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.272 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.182 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.297 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3212 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2959 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4360 ; 1.358 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6824 ; 0.781 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 7.786 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 496 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3580 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 690 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 506 ; 0.191 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3514 ; 0.238 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2143 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 98 ; 0.167 ; 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): 23 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.249 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.134 ; 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): 2002 ; 2.664 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3224 ; 4.062 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1210 ; 3.068 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1136 ; 4.613 ; 5.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 105 A 115 5 REMARK 3 1 B 105 B 115 5 REMARK 3 1 D 105 D 115 5 REMARK 3 2 A 123 A 165 5 REMARK 3 2 B 123 B 165 5 REMARK 3 2 D 123 D 165 5 REMARK 3 3 A 169 A 189 5 REMARK 3 3 B 169 B 189 5 REMARK 3 3 D 169 D 189 5 REMARK 3 4 A 198 A 241 5 REMARK 3 4 B 198 B 241 5 REMARK 3 4 D 198 D 241 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 679 ; 0.28 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 679 ; 0.35 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 D (A): 679 ; 0.26 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 1110 ; 0.92 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 1110 ; 0.83 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 D (A): 1110 ; 0.87 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 679 ; 1.12 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 679 ; 1.05 ; 2.00 REMARK 3 MEDIUM THERMAL 1 D (A**2): 679 ; 1.11 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 1110 ; 3.02 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 1110 ; 3.01 ; 10.00 REMARK 3 LOOSE THERMAL 1 D (A**2): 1110 ; 2.58 ; 10.00 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 105 A 241 REMARK 3 ORIGIN FOR THE GROUP (A): 21.8823 -10.5960 9.5902 REMARK 3 T TENSOR REMARK 3 T11: 0.1330 T22: 0.0601 REMARK 3 T33: 0.0790 T12: -0.0389 REMARK 3 T13: -0.0686 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 4.2543 L22: 3.9438 REMARK 3 L33: 2.7785 L12: -0.1118 REMARK 3 L13: 0.0958 L23: -0.5689 REMARK 3 S TENSOR REMARK 3 S11: -0.0755 S12: 0.1235 S13: -0.3330 REMARK 3 S21: -0.3809 S22: 0.1566 S23: 0.2893 REMARK 3 S31: 0.3841 S32: -0.2113 S33: -0.0811 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 : B 105 B 241 REMARK 3 ORIGIN FOR THE GROUP (A): 34.1973 -2.0520 26.9825 REMARK 3 T TENSOR REMARK 3 T11: 0.1736 T22: 0.1639 REMARK 3 T33: 0.0347 T12: -0.0566 REMARK 3 T13: -0.0612 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 3.4198 L22: 5.9176 REMARK 3 L33: 2.0265 L12: 1.7172 REMARK 3 L13: -0.4392 L23: -1.5950 REMARK 3 S TENSOR REMARK 3 S11: 0.3036 S12: -0.5015 S13: -0.0761 REMARK 3 S21: 0.8042 S22: -0.3742 S23: -0.2680 REMARK 3 S31: -0.1238 S32: 0.2278 S33: 0.0706 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 : D 105 D 241 REMARK 3 ORIGIN FOR THE GROUP (A): 19.7294 12.0103 15.2460 REMARK 3 T TENSOR REMARK 3 T11: 0.0554 T22: 0.0832 REMARK 3 T33: 0.2006 T12: 0.0327 REMARK 3 T13: 0.0696 T23: 0.0295 REMARK 3 L TENSOR REMARK 3 L11: 1.4855 L22: 4.8101 REMARK 3 L33: 3.3903 L12: 0.0799 REMARK 3 L13: 0.4699 L23: -0.1826 REMARK 3 S TENSOR REMARK 3 S11: 0.1271 S12: 0.0149 S13: 0.2119 REMARK 3 S21: 0.1743 S22: 0.1170 S23: 0.6413 REMARK 3 S31: -0.2278 S32: -0.4008 S33: -0.2441 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 1U5Y 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_1000023286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 RU200 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 : 23803 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 94.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27500 REMARK 200 FOR SHELL : 4.300 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: I23 STRUCTURE OF APRIL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.0, 1M LICL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 61.67200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.58300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.67200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.58300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 ASYMMETRIC UNIT CONTAINS THE BIOLOGICALLY RELEVANT REMARK 300 TRIMER 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 REMARK 350 TOTAL BURIED SURFACE AREA: 5290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D 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 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 GLY B 102 REMARK 465 SER B 103 REMARK 465 LYS B 104 REMARK 465 GLY D 102 REMARK 465 SER D 103 REMARK 465 LYS D 104 REMARK 465 MET D 191 REMARK 465 PRO D 192 REMARK 465 SER D 193 REMARK 465 ASP D 194 REMARK 465 PRO D 195 REMARK 465 ASP D 196 REMARK 465 ARG D 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 119 CG CD CE NZ REMARK 470 VAL A 165 CG1 CG2 REMARK 470 LYS B 119 CG CD CE NZ REMARK 470 VAL B 165 CG1 CG2 REMARK 470 PHE B 167 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 180 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 222 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 119 CG CD CE NZ REMARK 470 ASP D 121 CG OD1 OD2 REMARK 470 SER D 122 OG REMARK 470 VAL D 165 CG1 CG2 REMARK 470 PHE D 167 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR D 168 OG1 CG2 REMARK 470 GLN D 178 CG CD OE1 NE2 REMARK 470 ARG D 180 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 222 CG CD NE CZ NH1 NH2 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 121 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 144 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 164 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 214 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP B 214 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP D 123 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP D 144 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP D 214 CB - CG - OD2 ANGL. DEV. = 6.3 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 ALA A 120 -81.16 -40.72 REMARK 500 PHE A 167 -60.38 -10.38 REMARK 500 PRO A 221 45.69 -81.41 REMARK 500 SER B 122 -14.10 -141.82 REMARK 500 VAL B 165 -167.51 -105.26 REMARK 500 THR B 166 42.52 33.22 REMARK 500 GLN B 178 73.64 -69.11 REMARK 500 PRO B 192 -79.37 -100.20 REMARK 500 SER B 193 -59.65 -29.25 REMARK 500 ILE D 116 -159.77 -103.63 REMARK 500 THR D 117 -134.83 -127.09 REMARK 500 LYS D 119 -75.89 -45.28 REMARK 500 VAL D 165 43.57 -153.03 REMARK 500 PHE D 167 -100.93 -6.01 REMARK 500 MET D 169 -160.61 -129.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U5X RELATED DB: PDB REMARK 900 SAME PROTEIN CRYSTALLIZED IN SPACE GROUP I23 AT PH 5.0 REMARK 900 RELATED ID: 1U5Z RELATED DB: PDB REMARK 900 SAME PROTEIN CRYSTALLIZED IN SPACE GROUP I23 AT PH 8.5 DBREF 1U5Y A 104 241 UNP Q9D777 TNF13_MOUSE 104 241 DBREF 1U5Y B 104 241 UNP Q9D777 TNF13_MOUSE 104 241 DBREF 1U5Y D 104 241 UNP Q9D777 TNF13_MOUSE 104 241 SEQADV 1U5Y GLY A 102 UNP Q9D777 CLONING ARTIFACT SEQADV 1U5Y SER A 103 UNP Q9D777 CLONING ARTIFACT SEQADV 1U5Y GLY B 102 UNP Q9D777 CLONING ARTIFACT SEQADV 1U5Y SER B 103 UNP Q9D777 CLONING ARTIFACT SEQADV 1U5Y GLY D 102 UNP Q9D777 CLONING ARTIFACT SEQADV 1U5Y SER D 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 SEQRES 1 B 140 GLY SER LYS LYS HIS SER VAL LEU HIS LEU VAL PRO VAL SEQRES 2 B 140 ASN ILE THR SER LYS ALA ASP SER ASP VAL THR GLU VAL SEQRES 3 B 140 MET TRP GLN PRO VAL LEU ARG ARG GLY ARG GLY LEU GLU SEQRES 4 B 140 ALA GLN GLY ASP ILE VAL ARG VAL TRP ASP THR GLY ILE SEQRES 5 B 140 TYR LEU LEU TYR SER GLN VAL LEU PHE HIS ASP VAL THR SEQRES 6 B 140 PHE THR MET GLY GLN VAL VAL SER ARG GLU GLY GLN GLY SEQRES 7 B 140 ARG ARG GLU THR LEU PHE ARG CYS ILE ARG SER MET PRO SEQRES 8 B 140 SER ASP PRO ASP ARG ALA TYR ASN SER CYS TYR SER ALA SEQRES 9 B 140 GLY VAL PHE HIS LEU HIS GLN GLY ASP ILE ILE THR VAL SEQRES 10 B 140 LYS ILE PRO ARG ALA ASN ALA LYS LEU SER LEU SER PRO SEQRES 11 B 140 HIS GLY THR PHE LEU GLY PHE VAL LYS LEU SEQRES 1 D 140 GLY SER LYS LYS HIS SER VAL LEU HIS LEU VAL PRO VAL SEQRES 2 D 140 ASN ILE THR SER LYS ALA ASP SER ASP VAL THR GLU VAL SEQRES 3 D 140 MET TRP GLN PRO VAL LEU ARG ARG GLY ARG GLY LEU GLU SEQRES 4 D 140 ALA GLN GLY ASP ILE VAL ARG VAL TRP ASP THR GLY ILE SEQRES 5 D 140 TYR LEU LEU TYR SER GLN VAL LEU PHE HIS ASP VAL THR SEQRES 6 D 140 PHE THR MET GLY GLN VAL VAL SER ARG GLU GLY GLN GLY SEQRES 7 D 140 ARG ARG GLU THR LEU PHE ARG CYS ILE ARG SER MET PRO SEQRES 8 D 140 SER ASP PRO ASP ARG ALA TYR ASN SER CYS TYR SER ALA SEQRES 9 D 140 GLY VAL PHE HIS LEU HIS GLN GLY ASP ILE ILE THR VAL SEQRES 10 D 140 LYS ILE PRO ARG ALA ASN ALA LYS LEU SER LEU SER PRO SEQRES 11 D 140 HIS GLY THR PHE LEU GLY PHE VAL LYS LEU FORMUL 4 HOH *81(H2 O) HELIX 1 1 ASP A 194 ALA A 198 5 5 HELIX 2 2 ASP B 194 ALA B 198 5 5 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 GLY A 177 -1 N GLU A 176 O ILE A 215 SHEET 5 A 5 ARG A 180 ARG A 186 -1 O PHE A 185 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 ASN A 115 O MET A 128 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 LEU A 155 O VAL A 239 SHEET 8 B 8 ASN A 200 LEU A 210 -1 O LEU A 210 N GLY A 152 SHEET 1 C 2 THR A 168 MET A 169 0 SHEET 2 C 2 ARG A 189 SER A 190 -1 O ARG A 189 N MET A 169 SHEET 1 D 5 LEU B 139 GLN B 142 0 SHEET 2 D 5 ILE B 145 VAL B 148 -1 O ILE B 145 N GLN B 142 SHEET 3 D 5 ASP B 214 ILE B 220 -1 O ILE B 216 N VAL B 146 SHEET 4 D 5 VAL B 172 GLU B 176 -1 N SER B 174 O THR B 217 SHEET 5 D 5 GLU B 182 ARG B 186 -1 O PHE B 185 N VAL B 173 SHEET 1 E 8 LEU B 139 GLN B 142 0 SHEET 2 E 8 ILE B 145 VAL B 148 -1 O ILE B 145 N GLN B 142 SHEET 3 E 8 ASP B 214 ILE B 220 -1 O ILE B 216 N VAL B 146 SHEET 4 E 8 THR B 125 ARG B 135 -1 N THR B 125 O ILE B 220 SHEET 5 E 8 VAL B 108 THR B 117 -1 N THR B 117 O GLU B 126 SHEET 6 E 8 PHE B 235 LYS B 240 -1 O LEU B 236 N LEU B 111 SHEET 7 E 8 GLY B 152 LEU B 161 -1 N LEU B 155 O VAL B 239 SHEET 8 E 8 SER B 201 LEU B 210 -1 O LEU B 210 N GLY B 152 SHEET 1 F 5 MET D 128 ARG D 135 0 SHEET 2 F 5 VAL D 108 ASN D 115 -1 N VAL D 112 O GLN D 130 SHEET 3 F 5 PHE D 235 LYS D 240 -1 O LEU D 236 N LEU D 111 SHEET 4 F 5 GLY D 152 PHE D 162 -1 N LEU D 155 O VAL D 239 SHEET 5 F 5 ASN D 200 LEU D 210 -1 O ASN D 200 N PHE D 162 SHEET 1 G 4 THR D 125 GLU D 126 0 SHEET 2 G 4 ASP D 214 ILE D 220 -1 O ILE D 220 N THR D 125 SHEET 3 G 4 ILE D 145 VAL D 148 -1 N VAL D 146 O ILE D 216 SHEET 4 G 4 LEU D 139 GLN D 142 -1 N GLN D 142 O ILE D 145 SHEET 1 H 4 THR D 125 GLU D 126 0 SHEET 2 H 4 ASP D 214 ILE D 220 -1 O ILE D 220 N THR D 125 SHEET 3 H 4 VAL D 172 GLU D 176 -1 N VAL D 172 O LYS D 219 SHEET 4 H 4 ARG D 181 ARG D 186 -1 O PHE D 185 N VAL D 173 SSBOND 1 CYS A 187 CYS A 202 1555 1555 2.02 SSBOND 2 CYS B 187 CYS B 202 1555 1555 2.03 SSBOND 3 CYS D 187 CYS D 202 1555 1555 2.05 CRYST1 123.344 81.166 53.585 90.00 111.79 90.00 C 1 2 1 12 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 0.008107 0.000000 0.003241 0.00000 SCALE2 0.000000 0.012320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020098 0.00000 MASTER 435 0 0 2 41 0 0 6 0 0 0 33 END