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- PDB-2frg: Structure of the immunoglobulin-like domain of human TLT-1 -

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Basic information

Entry
Database: PDB / ID: 2frg
TitleStructure of the immunoglobulin-like domain of human TLT-1
Componentstrem-like transcript-1
KeywordsIMMUNE SYSTEM / immunoglobulin-like / beta-sandwich / cell surface receptor / triggering receptor / TREM-like / platelet receptor / ITIM
Function / homology
Function and homology information


platelet alpha granule / calcium-mediated signaling / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / nuclear speck / innate immune response / Golgi apparatus / cell surface / membrane / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Trem-like transcript 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsGattis, J.L. / Lubkowski, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The structure of the extracellular domain of triggering receptor expressed on myeloid cells like transcript-1 and evidence for a naturally occurring soluble fragment.
Authors: Gattis, J.L. / Washington, A.V. / Chisholm, M.M. / Quigley, L. / Szyk, A. / McVicar, D.W. / Lubkowski, J.
History
DepositionJan 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: trem-like transcript-1


Theoretical massNumber of molelcules
Total (without water)11,5231
Polymers11,5231
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.095, 79.981, 25.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11P-232-

HOH

21P-277-

HOH

DetailsCurrent biochemical and crystallographic evidence suggest that the biologically active form is monomeric.

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Components

#1: Antibody trem-like transcript-1


Mass: 11523.272 Da / Num. of mol.: 1 / Fragment: immunoglobulin-like domain 20-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLT-1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3RIL / References: UniProt: Q86YW5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Mother liquor contained 15-19% w/w PEG6000, 0.5M Na/K phosphate pH 5.6. Protein solution contained 10mg/ml TLT-1 in 20mM Tris pH 8. Protein and mother liquor were mixed in equal proportions ...Details: Mother liquor contained 15-19% w/w PEG6000, 0.5M Na/K phosphate pH 5.6. Protein solution contained 10mg/ml TLT-1 in 20mM Tris pH 8. Protein and mother liquor were mixed in equal proportions at 15 C, and hanging drops were suspended over mother liquor., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.54
SYNCHROTRONAPS 22-ID21.13
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEMay 24, 2005mirrors
MARRESEARCH2CCDJun 10, 2005monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2double-crystal Si(220) sagittal focusedSINGLE WAVELENGTHMx-ray1
1Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
21.131
ReflectionResolution: 1.19→30 Å / Num. all: 32052 / Num. obs: 31487 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.064 / Net I/σ(I): 25.9
Reflection shellResolution: 1.19→1.23 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.31 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Hybrid model containing structurally conserved residues of TREM-1 (1SMO chain A), NKp44(1HKF), and D1 domain of polymeric immunoglobulin receptor (1XED chain E).

1smo

1hkf

1xed


Resolution: 1.19→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.156 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19062 1547 4.9 %RANDOM
Rwork0.17644 ---
obs0.17711 29945 98.22 %-
all-31487 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.076 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.144 Å
Refinement stepCycle: LAST / Resolution: 1.19→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 0 152 958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022823
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9941119
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0323.42935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11815137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.156158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.2360
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2548
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1920.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4921.5539
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.112848
X-RAY DIFFRACTIONr_scbond_it3.0673311
X-RAY DIFFRACTIONr_scangle_it4.2364.5271
X-RAY DIFFRACTIONr_rigid_bond_restr1.76631853
X-RAY DIFFRACTIONr_sphericity_free6.9143152
X-RAY DIFFRACTIONr_sphericity_bonded2.88231582
LS refinement shellResolution: 1.19→1.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 108 -
Rwork0.28 1851 -
obs--83.47 %

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