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 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,VAGIN,DODSON
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) (%) : 100.00
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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1602 ; 3.077 ; 2.500
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1497 ; 4.711 ; 5.000
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 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 RCSB ID CODE IS RCSB030770.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
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 NI NI B 301 NE2 HIS A 106 1555 1555 2.56
LINK NI NI B 301 NE2 HIS B 106 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
(ATOM LINES ARE NOT SHOWN.)
END
