+Open data
-Basic information
Entry | Database: PDB / ID: 4q9v | ||||||
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Title | Crystal structure of TIPE3 | ||||||
Components | Tumor necrosis factor alpha-induced protein 8-like protein 3 | ||||||
Keywords | IMMUNE SYSTEM / helix / lipid transfer protein | ||||||
Function / homology | Function and homology information PI Metabolism / : / : / phosphatidylinositol transfer activity / phospholipid transport / regulation of lipid metabolic process / phospholipid metabolic process / phosphatidylinositol binding / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ...PI Metabolism / : / : / phosphatidylinositol transfer activity / phospholipid transport / regulation of lipid metabolic process / phospholipid metabolic process / phosphatidylinositol binding / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wu, J. / Zhang, X. / Chen, Y.H. / Shi, Y. | ||||||
Citation | Journal: Cancer Cell / Year: 2014 Title: TIPE3 Is the Transfer Protein of Lipid Second Messengers that Promote Cancer. Authors: Fayngerts, S.A. / Wu, J. / Oxley, C.L. / Liu, X. / Vourekas, A. / Cathopoulis, T. / Wang, Z. / Cui, J. / Liu, S. / Sun, H. / Lemmon, M.A. / Zhang, L. / Shi, Y. / Chen, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q9v.cif.gz | 172.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q9v.ent.gz | 139.2 KB | Display | PDB format |
PDBx/mmJSON format | 4q9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/4q9v ftp://data.pdbj.org/pub/pdb/validation_reports/q9/4q9v | HTTPS FTP |
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-Related structure data
Related structure data | 3f4mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21639.145 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 109-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP8L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GJ75 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 0.1M MES6.7,1.95M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 29427 / Num. obs: 29415 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F4M Resolution: 2.3→38.744 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 28.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.504 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→38.744 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: 3.3279 Å / Origin y: -22.6134 Å / Origin z: -40.9204 Å
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Refinement TLS group | Selection details: ALL |