PDB Short entry for 1U5Y 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 5 03-APR-24 1U5Y 1 SEQADV 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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