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Yorodumi- PDB-5v6c: Crystal Structure of the Second beta-Prism Domain of RbmC from V.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v6c | ||||||
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Title | Crystal Structure of the Second beta-Prism Domain of RbmC from V. cholerae | ||||||
Components | Hemolysin-related protein | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / beta-prism / glycan-binding domain | ||||||
Function / homology | Function and homology information Metalloprotease StcE, C-terminal / Beta/Gamma crystallin / Hemolysin, beta-prism lectin / Beta-prism lectin / FG-GAP-like repeat / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain superfamily / FG-GAP repeat ...Metalloprotease StcE, C-terminal / Beta/Gamma crystallin / Hemolysin, beta-prism lectin / Beta-prism lectin / FG-GAP-like repeat / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain superfamily / FG-GAP repeat / Integrin alpha, N-terminal / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Model details | apo form | ||||||
Authors | De, S. / Kaus, K. / Sinclair, S. / Case, B.C. / Olson, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: PLoS Pathog. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v6c.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v6c.ent.gz | 130.2 KB | Display | PDB format |
PDBx/mmJSON format | 5v6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/5v6c ftp://data.pdbj.org/pub/pdb/validation_reports/v6/5v6c | HTTPS FTP |
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-Related structure data
Related structure data | 5v6fC 5v6kC 1xezS 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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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14932.883 Da / Num. of mol.: 3 / Fragment: lectin domain, UNP residues 823-957 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_0930 / Plasmid: pNGFP-BC / Production host: Escherichia coli (E. coli) / Strain (production host): NEB T7 Express / References: UniProt: Q9KTH2 #2: Chemical | ChemComp-GOL / #3: 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: 2.33 Å3/Da / Density % sol: 47.14 % / Mosaicity: 0.68 ° |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Oct 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→16.53 Å / Num. obs: 21750 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.978 / Rmerge(I) obs: 0.347 / Rpim(I) all: 0.14 / Rrim(I) all: 0.375 / Net I/σ(I): 7.5 / Num. measured all: 154289 / Scaling rejects: 80 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.372 / Num. measured all: 13314 / Num. unique obs: 1994 / CC1/2: 0.624 / Rpim(I) all: 0.573 / Rrim(I) all: 1.489 / Net I/σ(I) obs: 2.1 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XEZ Resolution: 2.2→16.53 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 20.46 / 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: 68.03 Å2 / Biso mean: 20.0736 Å2 / Biso min: 5.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→16.53 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: 12
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