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- PDB-3bi9: Tim-4 -

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Basic information

Entry
Database: PDB / ID: 3bi9
TitleTim-4
ComponentsT-cell immunoglobulin and mucin domain-containing protein 4
KeywordsIMMUNE SYSTEM / BETA BARREL / IMMUNOGLOBULIN FOLD / IgV DOMAIN / TIM / Glycoprotein / Immunoglobulin domain / Membrane / Polymorphism / Transmembrane
Function / homology
Function and homology information


cytoskeletal rearrangement involved in phagocytosis, engulfment / apoptotic cell clearance / phosphatidylserine binding / membrane
Similarity search - Function
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / T-cell immunoglobulin and mucin domain-containing protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSantiago, C. / Ballesteros, A. / Kaplan, G.G. / Freeman, G.J. / Casasnovas, J.M.
CitationJournal: Immunity / Year: 2007
Title: Structures of T Cell Immunoglobulin Mucin Protein 4 Show a Metal-Ion-Dependent Ligand Binding Site where Phosphatidylserine Binds.
Authors: Santiago, C. / Ballesteros, A. / Martinez-Munoz, L. / Mellado, M. / Kaplan, G.G. / Freeman, G.J. / Casasnovas, J.M.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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_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
X: T-cell immunoglobulin and mucin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2384
Polymers13,0611
Non-polymers1773
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.270, 65.270, 57.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11X-118-

ACT

21X-118-

ACT

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Components

#1: Protein T-cell immunoglobulin and mucin domain-containing protein 4 / TIMD-4 / T-cell membrane protein 4 / TIM-4 / Spleen / mucin- containing / knockout of lymphotoxin ...TIMD-4 / T-cell membrane protein 4 / TIM-4 / Spleen / mucin- containing / knockout of lymphotoxin protein / SMUCKLER


Mass: 13061.049 Da / Num. of mol.: 1 / Fragment: N-TERMINAL CYS-RICH DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: KNOWLES SOLTER / Gene: Timd4, Tim4 / Plasmid: pET27B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6U7R4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na ACETATE, 30% PEG-2000 METHYLETHER, 5% PEG-400, 0.1 M AMMONIUM SULPHATE, 100 mM O-(n-OCTYL)-PHOSPHORYLCHOLINE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.95→25 Å / Num. all: 3238 / Num. obs: 3066 / % possible obs: 98.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 42.55 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 10.9 / Net I/σ(I): 6.7
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.8 / Num. unique all: 448 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TIM-2 HOMOLOGOUS MODEL

Resolution: 2.95→15 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 136 random
Rwork0.236 --
all-3129 -
obs-3036 -
Refinement stepCycle: LAST / Resolution: 2.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms893 0 12 11 916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7629
X-RAY DIFFRACTIONc_bond_d0.008

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