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- PDB-2re9: Crystal structure of TL1A at 2.1 A -

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Basic information

Entry
Database: PDB / ID: 2re9
TitleCrystal structure of TL1A at 2.1 A
ComponentsTNF superfamily ligand TL1A
KeywordsCYTOKINE / HORMONE/GROWTH FACTOR / VEGI / homotrimer / metal binding / Membrane / Transmembrane / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


TNFs bind their physiological receptors / activation of NF-kappaB-inducing kinase activity / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / cytokine activity / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / immune response / signaling receptor binding / signal transduction ...TNFs bind their physiological receptors / activation of NF-kappaB-inducing kinase activity / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / cytokine activity / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / immune response / signaling receptor binding / signal transduction / extracellular space / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 15 / Tumor necrosis factor ligand superfamily member 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJin, T.C. / Guo, F. / Kim, S. / Howard, A.J. / Zhang, Y.Z.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: X-ray crystal structure of TNF ligand family member TL1A at 2.1 A.
Authors: Jin, T. / Guo, F. / Kim, S. / Howard, A. / Zhang, Y.Z.
#1: Journal: To be Published
Title: Purification and crystallization of recombinant human TNF-like ligand TL1A
Authors: Jin, T.C. / Guo, F. / Kim, S. / Howard, A.J. / Zhang, Y.Z.
History
DepositionSep 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TNF superfamily ligand TL1A
B: TNF superfamily ligand TL1A
C: TNF superfamily ligand TL1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8686
Polymers61,6603
Non-polymers2083
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.911, 114.911, 119.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsAuthors state that biological unit is the same as asymmetric unit.

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Components

#1: Protein TNF superfamily ligand TL1A / Tumor necrosis factor (Ligand) superfamily / member 15


Mass: 20553.326 Da / Num. of mol.: 3 / Fragment: Soluble part: Residues 72-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF15 / Plasmid: pDEST14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NFE9, UniProt: O95150*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.86
Details: 0.2 M Magnesium formate, pH 6.86, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2007
RadiationMonochromator: ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46993 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.131 / Χ2: 1.002 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.96 / Num. unique all: 4595 / Χ2: 1.001 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A8M

1a8m


Resolution: 2.1→50 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2194 4.6 %Thin shells
Rwork0.198 ---
obs-43958 93.2 %-
Solvent computationBsol: 78.257 Å2
Displacement parametersBiso mean: 49.352 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 13 500 4458
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.349
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:glycerol.param

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