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Yorodumi- PDB-5y7d: Crystal structure of human Endothelial-overexpressed LPS associat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y7d | ||||||
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Title | Crystal structure of human Endothelial-overexpressed LPS associated factor 1 | ||||||
Components | Protein CXorf40A | ||||||
Keywords | HYDROLASE / endothelial-overexpressed LPS associated factor 1 / RNA binding domain / PUA domain | ||||||
Function / homology | Protein EOLA1/EOLA2 / ASCH / ASCH domain / regulation of interleukin-6 production / PUA-like superfamily / regulation of gene expression / Protein EOLA1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.71 Å | ||||||
Authors | Park, S.H. / Kim, M.J. / Park, J.S. / Kim, H.J. / Han, B.W. | ||||||
Citation | Journal: Molecules / Year: 2019 Title: Crystal Structure of Human EOLA1 Implies Its Possibility of RNA Binding. Authors: Kim, M. / Park, S.H. / Park, J.S. / Kim, H.J. / Han, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y7d.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y7d.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/5y7d ftp://data.pdbj.org/pub/pdb/validation_reports/y7/5y7d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18243.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXorf40A, CXorf40, EOLA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TE69 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 4.3M NaCl |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.709→47.89 Å / Num. obs: 24918 / % possible obs: 99.8 % / Redundancy: 29.4 % / Net I/σ(I): 53.11 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.71→32.933 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→32.933 Å
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Refine LS restraints |
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LS refinement shell |
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