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Yorodumi- PDB-6cf9: Crystal structure of soluble lytic transglycosylase Cj0843 of Cam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cf9 | ||||||
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Title | Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni at 2.3A resolution in I23 space group | ||||||
Components | Lytic transglycosylase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | ACETATE ION / : Function and homology information | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | van den Akker, F. / Kumar, V. | ||||||
Citation | Journal: PLoS ONE / Year: 2018 Title: Structural studies and molecular dynamics simulations suggest a processive mechanism of exolytic lytic transglycosylase from Campylobacter jejuni. Authors: Vijayaraghavan, J. / Kumar, V. / Krishnan, N.P. / Kaufhold, R.T. / Zeng, X. / Lin, J. / van den Akker, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cf9.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cf9.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 6cf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cf9_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 6cf9_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 6cf9_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 6cf9_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/6cf9 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/6cf9 | HTTPS FTP |
-Related structure data
Related structure data | 6cf8SC 6cfcC S: Starting model for refinement C: citing same article (ref.) |
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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: 61473.270 Da / Num. of mol.: 1 / Fragment: residues 18-540 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: BD28_04025 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L7J388 | ||
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#2: Chemical | ChemComp-PG0 / | ||
#3: Chemical | #4: 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: 3.92 Å3/Da / Density % sol: 68.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2 M Ammonium acetate, 0.1 M sodium acetate pH 4.6, and 30% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→126.34 Å / Num. obs: 42902 / % possible obs: 99.6 % / Redundancy: 40.4 % / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.28→2.35 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CF8 Resolution: 2.29→126.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.669 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.182 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.99 Å2 / Biso mean: 62.451 Å2 / Biso min: 37.54 Å2
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Refinement step | Cycle: final / Resolution: 2.29→126.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.289→2.348 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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