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Yorodumi- PDB-5cb0: Crystal structure and functional implications of the tandem-type ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cb0 | |||||||||
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Title | Crystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli | |||||||||
Components | Universal stress protein E | |||||||||
Keywords | UNKNOWN FUNCTION / UspE / UspA superfamily / Enterohemorrhagic Escherichia coli | |||||||||
Function / homology | Function and homology information single-species biofilm formation / bacterial-type flagellum-dependent cell motility / cellular response to hydrogen peroxide / cellular response to UV / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.207 Å | |||||||||
Authors | Xu, Y. / Quan, C.S. / Jin, X. / Jin, L. / Kim, J.S. / Guo, J. / Fan, S. / Ha, N.C. | |||||||||
Funding support | China, 2items
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Citation | Journal: Bmc Struct.Biol. / Year: 2016 Title: Crystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli. Authors: Xu, Y. / Guo, J. / Jin, X. / Kim, J.S. / Ji, Y. / Fan, S. / Ha, N.C. / Quan, C.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cb0.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cb0.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/5cb0 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/5cb0 | HTTPS FTP |
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-Related structure data
Related structure data | 3olqS 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: 35747.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: uspE, ydaA, b1333, JW1327 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAC0 #2: Chemical | |
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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: 3.1 Å3/Da / Density % sol: 60.37 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 288 K / Method: evaporation / pH: 6.5 Details: 10% 1.4-dioxane, 1.6 M ammonium sulfate, 0.1 M MES (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 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: Jun 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→19.9 Å / Num. all: 16684 / Num. obs: 16684 / % possible obs: 90.2 % / Redundancy: 3.6 % / Net I/σ(I): 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OLQ Resolution: 3.207→19.9 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.53 / Phase error: 29.47 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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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: 3.207→19.9 Å
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Refine LS restraints |
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LS refinement shell |
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