HEADER CYTOKINE 05-OCT-09 3K48 TITLE CRYSTAL STRUCTURE OF APRIL BOUND TO A PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13; COMPND 3 CHAIN: A, B, D; COMPND 4 FRAGMENT: RESIDUES 104-241; COMPND 5 SYNONYM: A PROLIFERATION-INDUCING LIGAND, APRIL; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PEPTIDE; COMPND 9 CHAIN: R, S, T; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: APRIL, TNFSF 13, TNFSF13; 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS CYTOKINE, TNFSF, CLEAVAGE ON PAIR OF BASIC RESIDUES, DISULFIDE BOND, KEYWDS 2 GLYCOPROTEIN, IMMUNE RESPONSE, SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR S.G.HYMOWITZ REVDAT 5 30-OCT-24 3K48 1 REMARK REVDAT 4 06-SEP-23 3K48 1 SEQADV REVDAT 3 10-AUG-11 3K48 1 JRNL REVDAT 2 13-JUL-11 3K48 1 VERSN REVDAT 1 24-NOV-09 3K48 0 JRNL AUTH N.C.GORDON,S.LIEN,J.JOHNSON,H.J.WALLWEBER,T.TRAN,B.CURRELL, JRNL AUTH 2 M.MATHIEU,C.QUAN,M.A.STAROVASNIK,S.G.HYMOWITZ,R.F.KELLEY JRNL TITL MULTIPLE NOVEL CLASSES OF APRIL-SPECIFIC RECEPTOR-BLOCKING JRNL TITL 2 PEPTIDES ISOLATED BY PHAGE DISPLAY. JRNL REF J.MOL.BIOL. V. 396 166 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 19945466 JRNL DOI 10.1016/J.JMB.2009.11.041 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 10257 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1143 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 675 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3613 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 50.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : -2.51000 REMARK 3 B33 (A**2) : 2.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.52000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.460 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.343 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.590 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.870 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3713 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2563 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5042 ; 1.252 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6159 ; 0.953 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 447 ; 6.842 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;32.822 ;22.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 604 ;15.047 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;17.592 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 546 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4105 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 815 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 624 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2669 ; 0.198 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1684 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2131 ; 0.079 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 55 ; 0.148 ; 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): 34 ; 0.237 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 74 ; 0.294 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.181 ; 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): 2901 ; 2.345 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 913 ; 0.494 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3645 ; 2.929 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1720 ; 1.788 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1397 ; 2.872 ; 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 105 A 241 4 REMARK 3 1 B 105 B 241 4 REMARK 3 1 D 105 D 241 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1839 ; 0.55 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 1839 ; 0.46 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 D (A): 1839 ; 0.50 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1839 ; 0.50 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 1839 ; 0.48 ; 2.00 REMARK 3 MEDIUM THERMAL 1 D (A**2): 1839 ; 0.49 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : R S T REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 R 2 R 14 4 REMARK 3 1 S 2 S 14 4 REMARK 3 1 T 2 T 14 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 R (A): 206 ; 0.17 ; 0.50 REMARK 3 MEDIUM POSITIONAL 2 S (A): 206 ; 0.12 ; 0.50 REMARK 3 MEDIUM POSITIONAL 2 T (A): 206 ; 0.14 ; 0.50 REMARK 3 MEDIUM THERMAL 2 R (A**2): 206 ; 0.40 ; 2.00 REMARK 3 MEDIUM THERMAL 2 S (A**2): 206 ; 0.32 ; 2.00 REMARK 3 MEDIUM THERMAL 2 T (A**2): 206 ; 0.30 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 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): 27.6862 -1.2135 27.8663 REMARK 3 T TENSOR REMARK 3 T11: -0.0441 T22: -0.0472 REMARK 3 T33: -0.0630 T12: -0.0037 REMARK 3 T13: -0.0119 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 3.3279 L22: 2.4045 REMARK 3 L33: 1.9890 L12: 0.3538 REMARK 3 L13: -0.1148 L23: -0.6674 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: -0.3394 S13: 0.0918 REMARK 3 S21: 0.2594 S22: -0.0570 S23: -0.1955 REMARK 3 S31: 0.0837 S32: 0.0160 S33: 0.0455 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): 15.0339 11.9639 13.7420 REMARK 3 T TENSOR REMARK 3 T11: -0.0404 T22: -0.0940 REMARK 3 T33: 0.0359 T12: 0.0253 REMARK 3 T13: -0.0356 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 2.0387 L22: 1.3170 REMARK 3 L33: 3.5400 L12: 0.0241 REMARK 3 L13: -0.1921 L23: -0.2486 REMARK 3 S TENSOR REMARK 3 S11: -0.1897 S12: 0.0774 S13: 0.1646 REMARK 3 S21: -0.0636 S22: 0.0323 S23: 0.1283 REMARK 3 S31: -0.2446 S32: -0.1471 S33: 0.1574 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): 17.1933 -10.7016 9.7295 REMARK 3 T TENSOR REMARK 3 T11: -0.0030 T22: -0.0671 REMARK 3 T33: -0.0674 T12: 0.0058 REMARK 3 T13: -0.0167 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 2.9805 L22: 1.7970 REMARK 3 L33: 1.9557 L12: -0.4621 REMARK 3 L13: 0.1383 L23: 0.1951 REMARK 3 S TENSOR REMARK 3 S11: 0.0693 S12: 0.1088 S13: -0.1169 REMARK 3 S21: -0.1622 S22: -0.0297 S23: 0.1271 REMARK 3 S31: 0.2157 S32: 0.0018 S33: -0.0396 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 1 R 16 REMARK 3 ORIGIN FOR THE GROUP (A): 15.5525 -20.4236 25.4938 REMARK 3 T TENSOR REMARK 3 T11: -0.0304 T22: -0.1019 REMARK 3 T33: -0.1062 T12: 0.0180 REMARK 3 T13: -0.0214 T23: 0.0364 REMARK 3 L TENSOR REMARK 3 L11: 8.2526 L22: 10.0223 REMARK 3 L33: 13.9338 L12: -5.6808 REMARK 3 L13: 3.7795 L23: 6.0344 REMARK 3 S TENSOR REMARK 3 S11: -0.4529 S12: -0.7111 S13: -0.0011 REMARK 3 S21: 0.7326 S22: 0.9038 S23: -0.1129 REMARK 3 S31: 0.7214 S32: -1.0590 S33: -0.4509 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : S 2 S 16 REMARK 3 ORIGIN FOR THE GROUP (A): 18.2380 10.8534 35.8997 REMARK 3 T TENSOR REMARK 3 T11: 0.0486 T22: -0.0421 REMARK 3 T33: -0.0020 T12: 0.0321 REMARK 3 T13: -0.0209 T23: -0.0410 REMARK 3 L TENSOR REMARK 3 L11: 0.1495 L22: 5.6986 REMARK 3 L33: 3.4265 L12: 0.9231 REMARK 3 L13: 0.7158 L23: 4.4188 REMARK 3 S TENSOR REMARK 3 S11: -0.4017 S12: -0.7249 S13: 0.7333 REMARK 3 S21: 0.9038 S22: -0.1907 S23: 0.1056 REMARK 3 S31: 0.1512 S32: -0.5322 S33: 0.5924 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : T 2 T 14 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4359 4.3682 8.3889 REMARK 3 T TENSOR REMARK 3 T11: -0.0357 T22: 0.1616 REMARK 3 T33: 0.1563 T12: 0.0153 REMARK 3 T13: -0.1029 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 2.0340 L22: 0.0008 REMARK 3 L33: 0.5080 L12: -0.0395 REMARK 3 L13: 1.0165 L23: -0.0197 REMARK 3 S TENSOR REMARK 3 S11: 0.3442 S12: 0.2276 S13: 0.0680 REMARK 3 S21: -0.2962 S22: -0.3590 S23: 0.8871 REMARK 3 S31: -0.0751 S32: -0.5774 S33: 0.0147 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 3K48 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055525. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11453 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10800 REMARK 200 FOR THE DATA SET : 12.4000 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50600 REMARK 200 FOR SHELL : 2.500 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: CHAIN A FROM PDB 1XU1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2UL DROPS OF PROTEIN (5 MG/MG. AT PH REMARK 280 9.7) WAS ADDED TO 2 UL OF 4M FORMATE. CRYSTALS FORMED REMARK 280 IMMEDIATELY, VAPOR DIFFUSION, HANGING 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 50.40550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.38550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.40550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.38550 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 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: 9690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, R, S, T 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 SER S 1 REMARK 465 GLU S 15 REMARK 465 HIS S 16 REMARK 465 SER T 1 REMARK 465 GLU T 15 REMARK 465 HIS T 16 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 PHE A 167 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE B 167 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE D 167 CG CD1 CD2 CE1 CE2 CZ 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 SER A 118 80.71 -161.91 REMARK 500 ASP A 123 53.08 -112.56 REMARK 500 PHE A 167 -83.76 45.08 REMARK 500 GLN A 178 35.52 73.55 REMARK 500 PRO A 221 31.60 -66.40 REMARK 500 ASP B 123 36.37 -96.89 REMARK 500 PHE B 167 -74.63 44.85 REMARK 500 PRO B 221 45.09 -78.92 REMARK 500 ASN D 115 133.04 -177.43 REMARK 500 SER D 118 100.32 -168.49 REMARK 500 PHE D 167 -72.16 41.89 REMARK 500 GLN D 212 131.36 -34.49 REMARK 500 PRO D 221 42.98 -73.37 REMARK 500 CYS R 14 60.98 -116.78 REMARK 500 GLU R 15 -125.00 87.99 REMARK 500 TRP S 8 33.29 -142.02 REMARK 500 TRP T 8 31.75 -141.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 3K48 A 104 241 UNP Q9D777 TNF13_MOUSE 104 241 DBREF 3K48 B 104 241 UNP Q9D777 TNF13_MOUSE 104 241 DBREF 3K48 D 104 241 UNP Q9D777 TNF13_MOUSE 104 241 DBREF 3K48 R 1 16 PDB 3K48 3K48 1 16 DBREF 3K48 S 1 16 PDB 3K48 3K48 1 16 DBREF 3K48 T 1 16 PDB 3K48 3K48 1 16 SEQADV 3K48 GLY A 102 UNP Q9D777 EXPRESSION TAG SEQADV 3K48 SER A 103 UNP Q9D777 EXPRESSION TAG SEQADV 3K48 GLY B 102 UNP Q9D777 EXPRESSION TAG SEQADV 3K48 SER B 103 UNP Q9D777 EXPRESSION TAG SEQADV 3K48 GLY D 102 UNP Q9D777 EXPRESSION TAG SEQADV 3K48 SER D 103 UNP Q9D777 EXPRESSION TAG 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 SEQRES 1 R 16 SER GLY TRP CYS ASP PRO ARG TRP TYR ASP PRO PHE MET SEQRES 2 R 16 CYS GLU HIS SEQRES 1 S 16 SER GLY TRP CYS ASP PRO ARG TRP TYR ASP PRO PHE MET SEQRES 2 S 16 CYS GLU HIS SEQRES 1 T 16 SER GLY TRP CYS ASP PRO ARG TRP TYR ASP PRO PHE MET SEQRES 2 T 16 CYS GLU HIS HELIX 1 1 ASP R 5 TYR R 9 5 5 HELIX 2 2 ASP R 10 CYS R 14 5 5 HELIX 3 3 ASP S 5 TYR S 9 5 5 HELIX 4 4 ASP S 10 CYS S 14 5 5 HELIX 5 5 ASP T 10 CYS T 14 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 THR A 168 GLU A 176 -1 N VAL A 172 O LYS A 219 SHEET 5 A 5 ARG A 181 SER A 190 -1 O ARG A 189 N MET A 169 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 VAL A 114 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 GLY A 206 N LEU A 156 SHEET 1 C 5 LEU B 139 GLN B 142 0 SHEET 2 C 5 ILE B 145 VAL B 148 -1 O ILE B 145 N GLN B 142 SHEET 3 C 5 ILE B 215 ILE B 220 -1 O ILE B 216 N VAL B 146 SHEET 4 C 5 THR B 168 GLY B 177 -1 N GLU B 176 O ILE B 215 SHEET 5 C 5 ARG B 180 SER B 190 -1 O ARG B 189 N MET B 169 SHEET 1 D 8 LEU B 139 GLN B 142 0 SHEET 2 D 8 ILE B 145 VAL B 148 -1 O ILE B 145 N GLN B 142 SHEET 3 D 8 ILE B 215 ILE B 220 -1 O ILE B 216 N VAL B 146 SHEET 4 D 8 THR B 125 ARG B 135 -1 N THR B 125 O ILE B 220 SHEET 5 D 8 VAL B 108 THR B 117 -1 N THR B 117 O GLU B 126 SHEET 6 D 8 PHE B 235 LYS B 240 -1 O LEU B 236 N LEU B 111 SHEET 7 D 8 GLY B 152 PHE B 162 -1 N LEU B 155 O VAL B 239 SHEET 8 D 8 ASN B 200 LEU B 210 -1 O LEU B 210 N GLY B 152 SHEET 1 E 5 GLU D 126 ARG D 135 0 SHEET 2 E 5 VAL D 108 THR D 117 -1 N ASN D 115 O MET D 128 SHEET 3 E 5 PHE D 235 LYS D 240 -1 O PHE D 238 N LEU D 109 SHEET 4 E 5 GLY D 152 PHE D 162 -1 N LEU D 155 O VAL D 239 SHEET 5 E 5 ASN D 200 LEU D 210 -1 O GLY D 206 N LEU D 156 SHEET 1 F 5 LEU D 139 GLN D 142 0 SHEET 2 F 5 ILE D 145 VAL D 148 -1 O ARG D 147 N GLU D 140 SHEET 3 F 5 ILE D 215 LYS D 219 -1 O ILE D 216 N VAL D 146 SHEET 4 F 5 THR D 168 GLY D 177 -1 N VAL D 172 O LYS D 219 SHEET 5 F 5 ARG D 180 SER D 190 -1 O ARG D 189 N MET D 169 SSBOND 1 CYS A 187 CYS A 202 1555 1555 2.04 SSBOND 2 CYS B 187 CYS B 202 1555 1555 2.03 SSBOND 3 CYS D 187 CYS D 202 1555 1555 2.03 SSBOND 4 CYS R 4 CYS R 14 1555 1555 2.05 SSBOND 5 CYS S 4 CYS S 14 1555 1555 2.04 SSBOND 6 CYS T 4 CYS T 14 1555 1555 2.07 CRYST1 100.811 84.771 55.562 90.00 99.45 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 0.009920 0.000000 0.001650 0.00000 SCALE2 0.000000 0.011796 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018245 0.00000