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- PDB-2o0o: Crystal structure of TL1A -

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Basic information

Entry
Database: PDB / ID: 2o0o
TitleCrystal structure of TL1A
ComponentsTNF superfamily ligand TL1A
KeywordsCYTOKINE / HORMONE/GROWTH FACTOR / VEGI / homotrimer / metal binding / cancer / angiogenesis / inflammation / 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 / cytokine activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / 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: 3 Å
AuthorsJin, T.C. / Kim, S. / Guo, F. / Howard, A.J. / Zhang, Y.Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: X-ray crystal structure of TNF ligand family member TL1A at 2.1A.
Authors: Jin, T. / Guo, F. / Kim, S. / Howard, A. / Zhang, Y.Z.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)61,5134
Polymers61,4893
Non-polymers241
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-45 kcal/mol
Surface area19180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.754, 116.754, 118.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 20496.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF15 / Plasmid: pRSFDuet-1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.2 M Magnesium Format, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Oct 22, 2006
RadiationMonochromator: ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→40 Å / Num. obs: 17122 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.311 / Χ2: 1.082 / Net I/σ(I): 7.1
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1659 / Χ2: 0.777 / % possible all: 99.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å36.99 Å
Translation3 Å36.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1A8M

1a8m


Resolution: 3→40 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 724 4.3 %Random
Rwork0.243 ---
all0.256 ---
obs0.247 15182 89.2 %-
Solvent computationBsol: 55.815 Å2
Displacement parametersBiso mean: 49.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.142 Å20 Å20 Å2
2--0.142 Å20 Å2
3----0.284 Å2
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 1 37 3591
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.377
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection% reflection
Rfree0.395 58 -
Rwork0.323 --
obs-1417 86.35 %
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

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