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- PDB-2qe3: Crystal structure of human tl1a extracellular domain -

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Basic information

Entry
Database: PDB / ID: 2qe3
TitleCrystal structure of human tl1a extracellular domain
ComponentsTNF superfamily ligand TL1A
KeywordsCYTOKINE / TL1A / TNFSF
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: 2.5 Å
AuthorsZhan, C. / Yan, Q. / Patskovsky, Y. / Shi, W. / Toro, R. / Bonanno, J. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2009
Title: Biochemical and structural characterization of the human TL1A ectodomain.
Authors: Zhan, C. / Yan, Q. / Patskovsky, Y. / Li, Z. / Toro, R. / Meyer, A. / Cheng, H. / Brenowitz, M. / Nathenson, S.G. / Almo, S.C.
History
DepositionJun 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
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_special_symmetry / 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 / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9101
Non-polymers351
Water1,06359
1
A: TNF superfamily ligand TL1A
hetero molecules

A: TNF superfamily ligand TL1A
hetero molecules

A: TNF superfamily ligand TL1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8366
Polymers62,7293
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7040 Å2
ΔGint-122 kcal/mol
Surface area16830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.404, 120.404, 120.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-701-

CL

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit.

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Components

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


Mass: 20909.748 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, residues 72-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF15 / Plasmid: PET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q8NFE9, UniProt: O95150*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 10 MM CACL2, 100 MM TRIS, PH 8.50, 20% METHONAL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2007 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10856 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 21.1 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.17 / Rsym value: 0.124 / Net I/σ(I): 3.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.96 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TNF

2tnf


Resolution: 2.5→19.8 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.456 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The extra density near residue ILE 145 at the three fold axis is not modelled.
RfactorNum. reflection% reflectionSelection details
Rfree0.26336 323 3 %RANDOM
Rwork0.20929 ---
obs0.21085 10462 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.137 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 1 59 1181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221173
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3551.9611596
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0625145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53824.15153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.23415199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.171155
X-RAY DIFFRACTIONr_chiral_restr0.1420.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02889
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.3594
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3550.5850
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.599
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.338
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.3723727
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.47331157
X-RAY DIFFRACTIONr_scbond_it11.9753509
X-RAY DIFFRACTIONr_scangle_it14.6973435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 26 -
Rwork0.395 735 -
obs--100 %

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