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- PDB-5v6k: Crystal Structure of the Second beta-Prism Domain of RbmC from V.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v6k | |||||||||
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Title | Crystal Structure of the Second beta-Prism Domain of RbmC from V. cholerae Bound to N-acetylglucosaminyl-beta-1,2-mannose | |||||||||
![]() | Hemolysin-related protein | |||||||||
![]() | SUGAR BINDING PROTEIN / ![]() | |||||||||
Function / homology | ![]() Metalloprotease StcE, C-terminal / Beta/Gamma crystallin / ![]() ![]() ![]() ![]() ![]() Similarity search - Domain/homology | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | De, S. / Kaus, K. / Sinclair, S. / Case, B.C. / Olson, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of mammalian glycan targeting by Vibrio cholerae cytolysin and biofilm proteins. Authors: De, S. / Kaus, K. / Sinclair, S. / Case, B.C. / Olson, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5v6cC ![]() 5v6fC ![]() 1xezS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14932.883 Da / Num. of mol.: 1 / Fragment: lectin domain, UNP residues 823-957 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_0930 / Plasmid: pNGFP-BC / Production host: ![]() ![]() ![]() |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose![]() Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-GOL / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.57 % / Mosaicity: 0.71 ° |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate, 2 M sodium sulfate, 1 mM N-acetylglucosaminyl-beta-1,2-mannose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→38.77 Å / Num. obs: 10585 / % possible obs: 91.9 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.044 / Rrim(I) all: 0.089 / Net I/σ(I): 11.4 / Num. measured all: 41463 / Scaling rejects: 114 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.477 / Num. measured all: 805 / Num. unique obs: 321 / CC1/2: 0.704 / Rpim(I) all: 0.37 / Rrim(I) all: 0.608 / Net I/σ(I) obs: 1.8 / % possible all: 47.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1XEZ Resolution: 1.8→30.652 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 20.82 / 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 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.33 Å2 / Biso mean: 16.8869 Å2 / Biso min: 8 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→30.652 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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