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- PDB-3mhd: Crystal structure of DCR3 -

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Basic information

Entry
Database: PDB / ID: 3mhd
TitleCrystal structure of DCR3
ComponentsTumor necrosis factor receptor superfamily member 6B
KeywordsIMMUNE SYSTEM / DCR3 / TNFR / DECOY RECEPTOR / GLYCOPROTEIN / SECRETED / RECEPTOR
Function / homology
Function and homology information


TNFs bind their physiological receptors / signaling receptor activity / negative regulation of apoptotic process / apoptotic process / extracellular space / extracellular region
Similarity search - Function
Tumor necrosis factor receptor 6B, N-terminal / : / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Ribbon / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsZhan, C. / Patskovsky, Y. / Yan, Q. / Li, Z. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Structure / Year: 2011
Title: Decoy Strategies: The Structure of TL1A:DcR3 Complex.
Authors: Zhan, C. / Patskovsky, Y. / Yan, Q. / Li, Z. / Ramagopal, U. / Cheng, H. / Brenowitz, M. / Hui, X. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Tumor necrosis factor receptor superfamily member 6B


Theoretical massNumber of molelcules
Total (without water)19,0441
Polymers19,0441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.019, 130.019, 96.026
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 6B / Decoy receptor for Fas ligand / Decoy receptor 3 / DcR3 / M68


Mass: 19044.217 Da / Num. of mol.: 1 / Fragment: UNP residues 30-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCR3, TNFRSF6B, TR6 / Plasmid: pMT/Bip/V5-His / Cell line (production host): S2 / Production host: DROSOPHILA (fruit flies) / References: UniProt: O95407

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M sodium acetate, 1mM CaCl2, 0.1M sodium citrate, 10% PEG 4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 8677 / Num. obs: 8677 / Redundancy: 7.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 1.2 / Num. unique all: 859

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K51

3k51


Resolution: 2.901→20 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.825 / SU B: 54.802 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R: 0.634 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The diffraction data were corrected for anisotropy
RfactorNum. reflection% reflectionSelection details
Rfree0.31481 169 2.7 %RANDOM
Rwork0.28535 ---
obs0.28619 6010 88.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.336 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.47 Å20 Å2
2--0.95 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.901→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 0 0 1004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9281450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8695133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42821.50953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.83815147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2891514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02858
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1290.3372
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.5662
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.541
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.320
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0330.51
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1441.5681
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.64921071
X-RAY DIFFRACTIONr_scbond_it10.8793429
X-RAY DIFFRACTIONr_scangle_it16.0044.5377
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.901→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 7 -
Rwork0.335 85 -
obs--18.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.05335.9611-1.43218.9908-1.765.52850.26680.16680.26391.15130.0522-0.3907-0.8320.3887-0.3190.4284-0.05480.13360.1542-0.06170.120542.81330.882540.8147
219.783211.03885.57515.52640.756115.61530.0970.9969-0.8862-0.6016-0.1984-0.55780.5952-1.02580.10140.2950.04750.22850.4509-0.04630.466517.6851-32.885440.7072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 113
2X-RAY DIFFRACTION2D114 - 170

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