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Yorodumi- PDB-6akv: Crystal structure of LysB4, the endolysin from Bacillus cereus-ta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6akv | ||||||
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Title | Crystal structure of LysB4, the endolysin from Bacillus cereus-targeting bacteriophage B4 | ||||||
Components | LysB4 | ||||||
Keywords | HYDROLASE / endolysin / LAS type enzyme / L-Alanoyl D-Glutamate endopeptidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus phage B4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hong, S. / Ha, N.-C. | ||||||
Citation | Journal: Mol. Cells / Year: 2019 Title: Crystal Structure of LysB4, an Endolysin fromBacillus cereus-Targeting Bacteriophage B4. Authors: Hong, S. / Son, B. / Ryu, S. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6akv.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6akv.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 6akv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6akv ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6akv | HTTPS FTP |
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-Related structure data
Related structure data | 2vo9S 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: 30083.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage B4 (virus) / Gene: lysB4, BCB4_0006 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: H9NAL3 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#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: 2.04 Å3/Da / Density % sol: 39.83 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.0 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 2% polyethylene glycol monomethyl ether 550 (PEGMME 550), 8 mM Tris(2-carboxyethyl)phosphine (TCEP) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 8863 / % possible obs: 91.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Net I/σ(I): 19.66 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 449 / CC1/2: 0.353 / Rpim(I) all: 0.222 / Rrim(I) all: 0.419 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VO9 Resolution: 2.4→28.092 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 22.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→28.092 Å
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Refine LS restraints |
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LS refinement shell |
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