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Yorodumi- PDB-5f7h: Human T-cell immunoglobulin and mucin domain protein 4 (hTIM-4) c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f7h | |||||||||
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Title | Human T-cell immunoglobulin and mucin domain protein 4 (hTIM-4) complex with phosphoserine | |||||||||
Components | T-cell immunoglobulin and mucin domain-containing protein 4 | |||||||||
Keywords | IMMUNE SYSTEM / complex / hTIM-4 / phosphoserine | |||||||||
Function / homology | Function and homology information cytoskeletal rearrangement involved in phagocytosis, engulfment / apoptotic cell clearance / phosphatidylserine binding / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Gao, G.F. / Lu, G. / Wang, H. / Qi, J. | |||||||||
Funding support | China, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f7h.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f7h.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 5f7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f7h_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
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Full document | 5f7h_full_validation.pdf.gz | 505.4 KB | Display | |
Data in XML | 5f7h_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 5f7h_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/5f7h ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f7h | HTTPS FTP |
-Related structure data
Related structure data | 5f70C 5f71C 5f7fC 3bi9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12667.476 Da / Num. of mol.: 6 / 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: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SEP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: hTIM-4 crystals were soaked in reservoir solution with the addition of 20 mM O-Phospho-L-serine (sigma-aldrich) and 5 mM CaCl2 for 20 h. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 30954 / % possible obs: 99.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 12.143 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.333 / Rsym value: 0.81 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BI9 Resolution: 2.5→48.216 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.216 Å
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Refine LS restraints |
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LS refinement shell |
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