HEADER CYTOKINE, HORMONE/GROWTH FACTOR RECEPTOR25-OCT-04 1XU2 TITLE THE CRYSTAL STRUCTURE OF APRIL BOUND TO BCMA 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 APRIL; COMPND 5 SYNONYM: A PROLIFERATION-INDUCING LIGAND, APRIL, TNFSF13B OR TALL-2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 17; COMPND 9 CHAIN: R, S, T; COMPND 10 FRAGMENT: BCMA ECD; COMPND 11 SYNONYM: B-CELL MATURATION PROTEIN, TNFFSF17; COMPND 12 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: PET32A (MODIFIED); SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: TNFRSF17, BCM, BCMA; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PZCT KEYWDS TNFSF, CYTOKINE, CRD, RECEPTOR, JELLY-ROLL, CYSTEINE-RICH, HORMONE- KEYWDS 2 GROWTH FACTOR RECEPTOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.G.HYMOWITZ,D.R.PATEL,H.J.A.WALLWEBER,S.RUNYON,M.YAN,J.YIN, AUTHOR 2 S.K.SHRIVER,N.C.GORDON,B.PAN,N.J.SKELTON,R.F.KELLEY,M.A.STAROVASNIK REVDAT 6 23-AUG-23 1XU2 1 REMARK LINK REVDAT 5 13-JUL-11 1XU2 1 VERSN REVDAT 4 24-FEB-09 1XU2 1 VERSN REVDAT 3 22-MAR-05 1XU2 1 JRNL REVDAT 2 23-NOV-04 1XU2 1 JRNL REVDAT 1 09-NOV-04 1XU2 0 JRNL AUTH S.G.HYMOWITZ,D.R.PATEL,H.J.A.WALLWEBER,S.RUNYON,M.YAN,J.YIN, JRNL AUTH 2 S.K.SHRIVER,N.C.GORDON,B.PAN,N.J.SKELTON,R.F.KELLEY, JRNL AUTH 3 M.A.STAROVASNIK JRNL TITL STRUCTURES OF APRIL-RECEPTOR COMPLEXES: LIKE BCMA, TACI JRNL TITL 2 EMPLOYS ONLY A SINGLE CYSTEINE-RICH DOMAIN FOR HIGH-AFFINITY JRNL TITL 3 LIGAND BINDING JRNL REF J.BIOL.CHEM. V. 280 7218 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15542592 JRNL DOI 10.1074/JBC.M411714200 REMARK 2 REMARK 2 RESOLUTION. 2.35 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) : 2.35 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 : 25409 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2856 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1680 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 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 : 4082 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 52.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : -0.05000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.294 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.209 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.871 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4187 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3760 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5686 ; 1.220 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8723 ; 0.762 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 513 ; 7.064 ; 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): 635 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4636 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 883 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 589 ; 0.180 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4165 ; 0.229 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2776 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 69 ; 0.133 ; 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): 9 ; 0.142 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 47 ; 0.201 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.232 ; 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): 2585 ; 2.575 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4189 ; 4.084 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1602 ; 3.077 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1497 ; 4.711 ; 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 : NULL 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): 11.4510 84.0327 4.6368 REMARK 3 T TENSOR REMARK 3 T11: 0.1011 T22: 0.1091 REMARK 3 T33: 0.1583 T12: -0.0141 REMARK 3 T13: -0.0341 T23: 0.1024 REMARK 3 L TENSOR REMARK 3 L11: 3.1461 L22: 2.7331 REMARK 3 L33: 2.5638 L12: -0.1252 REMARK 3 L13: 0.9115 L23: -0.2272 REMARK 3 S TENSOR REMARK 3 S11: 0.1006 S12: -0.2092 S13: -0.3960 REMARK 3 S21: 0.0627 S22: 0.0298 S23: 0.2027 REMARK 3 S31: 0.2755 S32: -0.2148 S33: -0.1305 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): 6.1167 105.9483 9.1820 REMARK 3 T TENSOR REMARK 3 T11: 0.0730 T22: 0.1615 REMARK 3 T33: 0.1655 T12: 0.0442 REMARK 3 T13: 0.0914 T23: 0.0533 REMARK 3 L TENSOR REMARK 3 L11: 2.6695 L22: 2.6706 REMARK 3 L33: 3.8296 L12: 0.4075 REMARK 3 L13: 0.9553 L23: -0.1667 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: -0.3133 S13: 0.2335 REMARK 3 S21: 0.3207 S22: -0.0449 S23: 0.4227 REMARK 3 S31: -0.2728 S32: -0.2242 S33: 0.0270 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): 26.0421 100.8884 -1.3595 REMARK 3 T TENSOR REMARK 3 T11: 0.0501 T22: 0.1274 REMARK 3 T33: 0.1136 T12: 0.0171 REMARK 3 T13: 0.0550 T23: 0.0814 REMARK 3 L TENSOR REMARK 3 L11: 2.9861 L22: 3.6954 REMARK 3 L33: 2.9577 L12: 0.1324 REMARK 3 L13: 0.9974 L23: -0.8393 REMARK 3 S TENSOR REMARK 3 S11: 0.0827 S12: 0.1931 S13: -0.0274 REMARK 3 S21: -0.0713 S22: -0.0891 S23: -0.4532 REMARK 3 S31: 0.1006 S32: 0.2988 S33: 0.0064 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 8 R 43 REMARK 3 ORIGIN FOR THE GROUP (A): -7.6636 83.1563 -9.5482 REMARK 3 T TENSOR REMARK 3 T11: 0.2739 T22: 0.2909 REMARK 3 T33: 0.3931 T12: -0.1393 REMARK 3 T13: -0.1688 T23: 0.1414 REMARK 3 L TENSOR REMARK 3 L11: 4.8149 L22: 9.5216 REMARK 3 L33: 14.3511 L12: 1.5843 REMARK 3 L13: 5.9660 L23: 4.6937 REMARK 3 S TENSOR REMARK 3 S11: 0.2382 S12: -0.0941 S13: -0.6291 REMARK 3 S21: -0.4535 S22: 0.1703 S23: 0.7924 REMARK 3 S31: 0.8782 S32: -0.5263 S33: -0.4085 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 6 S 42 REMARK 3 ORIGIN FOR THE GROUP (A): 0.9554 117.8873 -10.0897 REMARK 3 T TENSOR REMARK 3 T11: 0.2506 T22: 0.3033 REMARK 3 T33: 0.4320 T12: 0.0712 REMARK 3 T13: -0.1136 T23: 0.1626 REMARK 3 L TENSOR REMARK 3 L11: 9.2180 L22: 10.6111 REMARK 3 L33: 11.1624 L12: -3.9994 REMARK 3 L13: 1.4052 L23: -0.4374 REMARK 3 S TENSOR REMARK 3 S11: -0.0251 S12: 0.3173 S13: 0.2861 REMARK 3 S21: -0.6638 S22: 0.0771 S23: 1.4078 REMARK 3 S31: -0.5072 S32: -1.1028 S33: -0.0520 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 8 T 42 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3902 94.1774 -23.5163 REMARK 3 T TENSOR REMARK 3 T11: 0.5681 T22: 0.5537 REMARK 3 T33: 0.1712 T12: -0.0691 REMARK 3 T13: 0.1130 T23: -0.0916 REMARK 3 L TENSOR REMARK 3 L11: 9.8575 L22: 6.2674 REMARK 3 L33: 21.7778 L12: 4.1672 REMARK 3 L13: -1.6925 L23: -4.1417 REMARK 3 S TENSOR REMARK 3 S11: -0.4791 S12: 1.7580 S13: -0.3046 REMARK 3 S21: -1.6534 S22: 0.6037 S23: -0.6857 REMARK 3 S31: 0.4978 S32: 0.0757 S33: -0.1245 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 1XU2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030770. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-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) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98040 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28292 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42500 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: APRIL ALONE (1U5Z) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION: 0.1M MES, 5% PEG 8000, REMARK 280 10% PEG 1000, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.39333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.78667 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 45.59000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 75.98333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.19667 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 ASSYMMETRIC UNIT CONTAINS THE BIOLOGICALLY RELEVANT REMARK 300 ASSEMBLY OF A TRIMER OF APRIL BOUND TO 3 COPIES OF BCMA 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: 10580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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 LYS A 104 REMARK 465 LYS B 104 REMARK 465 LYS D 104 REMARK 465 ALA R 5 REMARK 465 GLY R 6 REMARK 465 GLN R 7 REMARK 465 SER R 44 REMARK 465 VAL R 45 REMARK 465 THR R 46 REMARK 465 ASN R 47 REMARK 465 SER R 48 REMARK 465 VAL R 49 REMARK 465 LYS R 50 REMARK 465 GLY R 51 REMARK 465 ALA S 5 REMARK 465 ALA S 43 REMARK 465 SER S 44 REMARK 465 VAL S 45 REMARK 465 THR S 46 REMARK 465 ASN S 47 REMARK 465 SER S 48 REMARK 465 VAL S 49 REMARK 465 LYS S 50 REMARK 465 GLY S 51 REMARK 465 ALA T 5 REMARK 465 GLY T 6 REMARK 465 GLN T 7 REMARK 465 ALA T 43 REMARK 465 SER T 44 REMARK 465 VAL T 45 REMARK 465 THR T 46 REMARK 465 ASN T 47 REMARK 465 SER T 48 REMARK 465 VAL T 49 REMARK 465 LYS T 50 REMARK 465 GLY T 51 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 ARG S 39 CG CD NE CZ NH1 NH2 REMARK 470 GLN T 38 CG CD OE1 NE2 REMARK 470 ARG T 39 CG CD NE CZ NH1 NH2 REMARK 470 ASN T 42 CG OD1 ND2 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 O HOH A 2 O HOH A 38 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN T 42 C ASN T 42 O 0.240 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 PRO A 221 46.87 -72.17 REMARK 500 ASP B 123 55.66 -114.89 REMARK 500 ARG B 180 106.71 -170.12 REMARK 500 PRO B 221 42.82 -74.03 REMARK 500 ALA D 120 -83.92 -54.12 REMARK 500 ASP D 123 60.86 -117.90 REMARK 500 ARG D 137 -149.05 -119.47 REMARK 500 PRO D 221 42.72 -72.56 REMARK 500 ASN R 31 -121.45 48.75 REMARK 500 ASN R 42 -68.23 -92.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 106 NE2 REMARK 620 2 HIS B 106 NE2 83.5 REMARK 620 3 HIS D 106 NE2 75.7 108.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XU1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APRIL BOUND TO TACI REMARK 900 RELATED ID: 1U5X RELATED DB: PDB REMARK 900 APRIL REMARK 900 RELATED ID: 1U5Y RELATED DB: PDB REMARK 900 APRIL REMARK 900 RELATED ID: 1U5Z RELATED DB: PDB REMARK 900 APRIL REMARK 900 RELATED ID: 1XUT RELATED DB: PDB DBREF 1XU2 A 104 241 UNP Q9D777 TNF13_MOUSE 104 241 DBREF 1XU2 B 104 241 UNP Q9D777 TNF13_MOUSE 104 241 DBREF 1XU2 D 104 241 UNP Q9D777 TNF13_MOUSE 104 241 DBREF 1XU2 R 5 51 UNP Q02223 TNR17_HUMAN 5 51 DBREF 1XU2 S 5 51 UNP Q02223 TNR17_HUMAN 5 51 DBREF 1XU2 T 5 51 UNP Q02223 TNR17_HUMAN 5 51 SEQRES 1 A 138 LYS LYS HIS SER VAL LEU HIS LEU VAL PRO VAL ASN ILE SEQRES 2 A 138 THR SER LYS ALA ASP SER ASP VAL THR GLU VAL MET TRP SEQRES 3 A 138 GLN PRO VAL LEU ARG ARG GLY ARG GLY LEU GLU ALA GLN SEQRES 4 A 138 GLY ASP ILE VAL ARG VAL TRP ASP THR GLY ILE TYR LEU SEQRES 5 A 138 LEU TYR SER GLN VAL LEU PHE HIS ASP VAL THR PHE THR SEQRES 6 A 138 MET GLY GLN VAL VAL SER ARG GLU GLY GLN GLY ARG ARG SEQRES 7 A 138 GLU THR LEU PHE ARG CYS ILE ARG SER MET PRO SER ASP SEQRES 8 A 138 PRO ASP ARG ALA TYR ASN SER CYS TYR SER ALA GLY VAL SEQRES 9 A 138 PHE HIS LEU HIS GLN GLY ASP ILE ILE THR VAL LYS ILE SEQRES 10 A 138 PRO ARG ALA ASN ALA LYS LEU SER LEU SER PRO HIS GLY SEQRES 11 A 138 THR PHE LEU GLY PHE VAL LYS LEU SEQRES 1 B 138 LYS LYS HIS SER VAL LEU HIS LEU VAL PRO VAL ASN ILE SEQRES 2 B 138 THR SER LYS ALA ASP SER ASP VAL THR GLU VAL MET TRP SEQRES 3 B 138 GLN PRO VAL LEU ARG ARG GLY ARG GLY LEU GLU ALA GLN SEQRES 4 B 138 GLY ASP ILE VAL ARG VAL TRP ASP THR GLY ILE TYR LEU SEQRES 5 B 138 LEU TYR SER GLN VAL LEU PHE HIS ASP VAL THR PHE THR SEQRES 6 B 138 MET GLY GLN VAL VAL SER ARG GLU GLY GLN GLY ARG ARG SEQRES 7 B 138 GLU THR LEU PHE ARG CYS ILE ARG SER MET PRO SER ASP SEQRES 8 B 138 PRO ASP ARG ALA TYR ASN SER CYS TYR SER ALA GLY VAL SEQRES 9 B 138 PHE HIS LEU HIS GLN GLY ASP ILE ILE THR VAL LYS ILE SEQRES 10 B 138 PRO ARG ALA ASN ALA LYS LEU SER LEU SER PRO HIS GLY SEQRES 11 B 138 THR PHE LEU GLY PHE VAL LYS LEU SEQRES 1 D 138 LYS LYS HIS SER VAL LEU HIS LEU VAL PRO VAL ASN ILE SEQRES 2 D 138 THR SER LYS ALA ASP SER ASP VAL THR GLU VAL MET TRP SEQRES 3 D 138 GLN PRO VAL LEU ARG ARG GLY ARG GLY LEU GLU ALA GLN SEQRES 4 D 138 GLY ASP ILE VAL ARG VAL TRP ASP THR GLY ILE TYR LEU SEQRES 5 D 138 LEU TYR SER GLN VAL LEU PHE HIS ASP VAL THR PHE THR SEQRES 6 D 138 MET GLY GLN VAL VAL SER ARG GLU GLY GLN GLY ARG ARG SEQRES 7 D 138 GLU THR LEU PHE ARG CYS ILE ARG SER MET PRO SER ASP SEQRES 8 D 138 PRO ASP ARG ALA TYR ASN SER CYS TYR SER ALA GLY VAL SEQRES 9 D 138 PHE HIS LEU HIS GLN GLY ASP ILE ILE THR VAL LYS ILE SEQRES 10 D 138 PRO ARG ALA ASN ALA LYS LEU SER LEU SER PRO HIS GLY SEQRES 11 D 138 THR PHE LEU GLY PHE VAL LYS LEU SEQRES 1 R 47 ALA GLY GLN CYS SER GLN ASN GLU TYR PHE ASP SER LEU SEQRES 2 R 47 LEU HIS ALA CYS ILE PRO CYS GLN LEU ARG CYS SER SER SEQRES 3 R 47 ASN THR PRO PRO LEU THR CYS GLN ARG TYR CYS ASN ALA SEQRES 4 R 47 SER VAL THR ASN SER VAL LYS GLY SEQRES 1 S 47 ALA GLY GLN CYS SER GLN ASN GLU TYR PHE ASP SER LEU SEQRES 2 S 47 LEU HIS ALA CYS ILE PRO CYS GLN LEU ARG CYS SER SER SEQRES 3 S 47 ASN THR PRO PRO LEU THR CYS GLN ARG TYR CYS ASN ALA SEQRES 4 S 47 SER VAL THR ASN SER VAL LYS GLY SEQRES 1 T 47 ALA GLY GLN CYS SER GLN ASN GLU TYR PHE ASP SER LEU SEQRES 2 T 47 LEU HIS ALA CYS ILE PRO CYS GLN LEU ARG CYS SER SER SEQRES 3 T 47 ASN THR PRO PRO LEU THR CYS GLN ARG TYR CYS ASN ALA SEQRES 4 T 47 SER VAL THR ASN SER VAL LYS GLY HET NI B 301 1 HETNAM NI NICKEL (II) ION FORMUL 7 NI NI 2+ FORMUL 8 HOH *36(H2 O) HELIX 1 1 ASP A 194 ARG A 197 5 4 HELIX 2 2 GLN R 25 ARG R 27 5 3 HELIX 3 3 PRO R 34 THR R 36 5 3 HELIX 4 4 CYS R 37 ALA R 43 1 7 HELIX 5 5 GLN S 25 CYS S 28 5 4 HELIX 6 6 CYS S 37 ASN S 42 1 6 HELIX 7 7 GLN T 25 CYS T 28 5 4 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 GLU A 176 O ILE A 215 SHEET 5 A 5 ARG A 181 SER A 190 -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 THR A 117 O GLU A 126 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 HIS A 163 -1 N LEU A 155 O VAL A 239 SHEET 8 B 8 TYR A 199 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 ARG B 147 N GLU B 140 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 GLU B 176 -1 N GLU B 176 O ILE B 215 SHEET 5 C 5 ARG B 181 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 ARG B 147 N GLU B 140 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 ASN B 115 O MET B 128 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 GLY B 206 N LEU B 156 SHEET 1 E 5 LEU D 139 GLN D 142 0 SHEET 2 E 5 ILE D 145 VAL D 148 -1 O ARG D 147 N GLU D 140 SHEET 3 E 5 ILE D 215 ILE D 220 -1 O ILE D 216 N VAL D 146 SHEET 4 E 5 THR D 168 GLU D 176 -1 N VAL D 172 O LYS D 219 SHEET 5 E 5 ARG D 181 SER D 190 -1 O LEU D 184 N VAL D 173 SHEET 1 F 8 LEU D 139 GLN D 142 0 SHEET 2 F 8 ILE D 145 VAL D 148 -1 O ARG D 147 N GLU D 140 SHEET 3 F 8 ILE D 215 ILE D 220 -1 O ILE D 216 N VAL D 146 SHEET 4 F 8 THR D 125 ARG D 135 -1 N THR D 125 O ILE D 220 SHEET 5 F 8 VAL D 108 THR D 117 -1 N HIS D 110 O VAL D 132 SHEET 6 F 8 PHE D 235 LYS D 240 -1 O LEU D 236 N LEU D 111 SHEET 7 F 8 GLY D 152 HIS D 163 -1 N LEU D 155 O VAL D 239 SHEET 8 F 8 TYR D 199 LEU D 210 -1 O GLY D 206 N LEU D 156 SHEET 1 G 2 GLU R 12 ASP R 15 0 SHEET 2 G 2 ALA R 20 PRO R 23 -1 O ALA R 20 N ASP R 15 SHEET 1 H 2 GLU S 12 ASP S 15 0 SHEET 2 H 2 ALA S 20 PRO S 23 -1 O ALA S 20 N ASP S 15 SHEET 1 I 2 GLU T 12 ASP T 15 0 SHEET 2 I 2 ALA T 20 PRO T 23 -1 O ILE T 22 N TYR T 13 SSBOND 1 CYS A 187 CYS A 202 1555 1555 2.03 SSBOND 2 CYS B 187 CYS B 202 1555 1555 2.04 SSBOND 3 CYS D 187 CYS D 202 1555 1555 2.05 SSBOND 4 CYS R 8 CYS R 21 1555 1555 2.05 SSBOND 5 CYS R 24 CYS R 37 1555 1555 2.10 SSBOND 6 CYS R 28 CYS R 41 1555 1555 2.06 SSBOND 7 CYS S 8 CYS S 21 1555 1555 2.08 SSBOND 8 CYS S 24 CYS S 37 1555 1555 2.07 SSBOND 9 CYS S 28 CYS S 41 1555 1555 2.05 SSBOND 10 CYS T 8 CYS T 21 1555 1555 2.05 SSBOND 11 CYS T 24 CYS T 37 1555 1555 2.07 SSBOND 12 CYS T 28 CYS T 41 1555 1555 2.06 LINK NE2 HIS A 106 NI NI B 301 1555 1555 2.56 LINK NE2 HIS B 106 NI NI B 301 1555 1555 2.18 LINK NI NI B 301 NE2 HIS D 106 1555 1555 2.34 SITE 1 AC1 3 HIS A 106 HIS B 106 HIS D 106 CRYST1 114.294 114.294 91.180 90.00 90.00 120.00 P 61 18 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 0.008749 0.005051 0.000000 0.00000 SCALE2 0.000000 0.010103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010967 0.00000