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- PDB-5f7f: Human T-cell immunoglobulin and mucin domain protein 4 (hTIM-4) -

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Basic information

Entry
Database: PDB / ID: 5f7f
TitleHuman T-cell immunoglobulin and mucin domain protein 4 (hTIM-4)
ComponentsT-cell immunoglobulin and mucin domain-containing protein 4
KeywordsIMMUNE SYSTEM / hTIM-4
Function / homology
Function and homology information


cytoskeletal rearrangement involved in phagocytosis, engulfment / apoptotic cell clearance / phosphatidylserine binding / extracellular region / plasma 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
T-cell immunoglobulin and mucin domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsGao, G.F. / Lu, G. / Wang, H. / Qi, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81590761 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08020100 China
CitationJournal: Chin.Sci.Bull. / Year: 2015
Title: Crystal structures of human TIM members: Ebolavirus entry-enhancing receptors
Authors: Wang, H. / Qi, J.X. / Liu, N.N.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell immunoglobulin and mucin domain-containing protein 4
B: T-cell immunoglobulin and mucin domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)25,3352
Polymers25,3352
Non-polymers00
Water4,882271
1
A: T-cell immunoglobulin and mucin domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)12,6671
Polymers12,6671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T-cell immunoglobulin and mucin domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)12,6671
Polymers12,6671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.485, 43.780, 44.726
Angle α, β, γ (deg.)77.32, 86.78, 85.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein T-cell immunoglobulin and mucin domain-containing protein 4 / TIMD-4 / T-cell immunoglobulin mucin receptor 4 / TIM-4 / T-cell membrane protein 4


Mass: 12667.476 Da / Num. of mol.: 2 / Fragment: UNP residues 24-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMD4, TIM4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96H15
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M phosphate/citrate, 40%(v/v) PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 34370 / % possible obs: 96.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 24.14
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5.82 / Rsym value: 0.283 / % possible all: 94.6

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Processing

Software
NameVersionClassification
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PHENIX1.9_1692refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BI9

3bi9


Resolution: 1.502→27.633 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 1726 5.03 %
Rwork0.1716 --
obs0.1725 34342 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.502→27.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 0 271 2037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091813
X-RAY DIFFRACTIONf_angle_d1.1952451
X-RAY DIFFRACTIONf_dihedral_angle_d12.575673
X-RAY DIFFRACTIONf_chiral_restr0.045277
X-RAY DIFFRACTIONf_plane_restr0.005312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5016-1.54580.21811410.19122577X-RAY DIFFRACTION91
1.5458-1.59570.16841260.1762721X-RAY DIFFRACTION94
1.5957-1.65270.22011420.17142653X-RAY DIFFRACTION95
1.6527-1.71890.19351630.16722707X-RAY DIFFRACTION96
1.7189-1.79710.20381490.16792721X-RAY DIFFRACTION96
1.7971-1.89180.2061270.16492758X-RAY DIFFRACTION96
1.8918-2.01030.1691400.16022723X-RAY DIFFRACTION96
2.0103-2.16550.16311370.16452769X-RAY DIFFRACTION97
2.1655-2.38330.19241700.16652729X-RAY DIFFRACTION97
2.3833-2.72790.19311560.17832760X-RAY DIFFRACTION97
2.7279-3.43580.18891370.1732776X-RAY DIFFRACTION97
3.4358-27.63790.1911380.17612722X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -9.5723 Å / Origin y: 15.8739 Å / Origin z: -12.2839 Å
111213212223313233
T0.0824 Å20.0003 Å20.0047 Å2-0.0948 Å20.0027 Å2--0.0912 Å2
L0.0719 °20.0406 °20.1157 °2-0.3503 °20.1587 °2--0.2333 °2
S-0.0193 Å °0.0181 Å °0.013 Å °0.0067 Å °0.0166 Å °0.011 Å °0.0002 Å °0.0166 Å °0.001 Å °
Refinement TLS groupSelection details: all

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