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Yorodumi- PDB-4dxz: crystal structure of a PliG-Ec mutant, a periplasmic lysozyme inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dxz | ||||||
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Title | crystal structure of a PliG-Ec mutant, a periplasmic lysozyme inhibitor of g-type lysozyme from Escherichia coli | ||||||
Components | Inhibitor of g-type lysozyme | ||||||
Keywords | HYDROLASE INHIBITOR / lysozyme inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å | ||||||
Authors | Leysen, S. / Vanheuverzwijn, S. / Van Asten, K. / Vanderkelen, L. / Michiels, C.W. / Strelkov, S.V. | ||||||
Citation | Journal: To be Published Title: crystal structure of a PliG-Ec mutant, a periplasmic lysozyme inhibitor of g-type lysozyme from Escherichia coli Authors: Leysen, S. / Vandekelen, L. / Michiels, C.W. / Strelkov, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dxz.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dxz.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 4dxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/4dxz ftp://data.pdbj.org/pub/pdb/validation_reports/dx/4dxz | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12668.682 Da / Num. of mol.: 1 / Mutation: L75M, L112M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pliG, ycgK, b1178, JW1167 / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76002 | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 1.98 Å3/Da / Density % sol: 37.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 0.1M sodium propionate/sodium cacodylate/BIS-TRIS propane pH5.25, 25% w/v PEG1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9797 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2010 |
Radiation | Monochromator: Bartels Monochromomator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→56.81 Å / Num. all: 39476 / Num. obs: 38149 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rsym value: 0.046 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 3941 / Rsym value: 0.432 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.25→40.158 Å / SU ML: 0.1 / σ(F): 0 / Phase error: 17.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.896 Å2 / ksol: 0.459 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.25→40.158 Å
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Refine LS restraints |
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LS refinement shell |
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