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Yorodumi- PDB-3wa1: Crystal structure of BinB: A receptor binding component of the bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wa1 | ||||||
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Title | Crystal structure of BinB: A receptor binding component of the binary toxin from Lysinibacillus sphaericus | ||||||
Components | BinB protein | ||||||
Keywords | TOXIN / A-B TOXIN / BINARY TOXIN | ||||||
Function / homology | Function and homology information spore wall / sporulation resulting in formation of a cellular spore / : / toxin activity Similarity search - Function | ||||||
Biological species | Lysinibacillus sphaericus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Srisucharitpanit, K. / Yao, M. / Chimnaronk, S. / Promdonkoy, B. / Boonserm, P. / Tanaka, I. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Crystal structure of BinB: A receptor binding component of the binary toxin from Lysinibacillus sphaericus Authors: Srisucharitpanit, K. / Yao, M. / Promdonkoy, B. / Chimnaronk, S. / Tanaka, I. / Boonserm, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wa1.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wa1.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 3wa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/3wa1 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/3wa1 | 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: 44800.152 Da / Num. of mol.: 1 / Fragment: ACTIVATE DOMAIN, UNP RESIDUES 19-407 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lysinibacillus sphaericus (bacteria) / Strain: 2297 / Gene: binB / Plasmid: pET-28b(+)-BinB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q7B2I6, UniProt: P18568*PLUS |
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#2: 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: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8 Details: 0.1M TRIS-HCL PH8.0, 0.2M LITHIUM SULFATE, 12% PEG 4000, VAPOR DIFFUSION, TEMPERATURE 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 8, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→28.99 Å / Num. all: 42536 / Num. obs: 42536 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.12 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 6069 / Rsym value: 0.433 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→24.64 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.181 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→24.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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