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Yorodumi- PDB-4dzg: Crystal structure of Aeromonas hydrophila PliG, a periplasmic lys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dzg | ||||||
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Title | Crystal structure of Aeromonas hydrophila PliG, a periplasmic lysozyme inhibitor of g-type lysozyme | ||||||
Components | PliG | ||||||
Keywords | HYDROLASE INHIBITOR / lysozyme inhibitor / g-type lysozyme binding | ||||||
Function / homology | Jelly Rolls - #380 / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Aeromonas hydrophila subsp. hydrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Leysen, S. / Theuwis, V. / Vanderkelen, L. / Michiels, C.W. / Strelkov, S.V. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Structural characterization of the PliG lysozyme inhibitor family. Authors: Leysen, S. / Vanderkelen, L. / Van Asten, K. / Vanheuverzwijn, S. / Theuwis, V. / 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 | 4dzg.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dzg.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/4dzg ftp://data.pdbj.org/pub/pdb/validation_reports/dz/4dzg | HTTPS FTP |
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-Related 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: 12150.683 Da / Num. of mol.: 1 / Fragment: UNP residues 22-134 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila subsp. hydrophila (bacteria) Strain: ATCC 7966 / NCIB 9240 / Gene: AHA_0125 / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0KEJ7 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 4.31 Å3/Da / Density % sol: 71.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate pH6.5, 1M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 26, 2011 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→19.06 Å / Num. all: 13867 / Num. obs: 13867 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rsym value: 0.078 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.02→2.13 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1862 / Rsym value: 0.0678 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→18.317 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 19.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.64 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.02→18.317 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.573 Å / Origin y: -17.106 Å / Origin z: 18.7633 Å
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Refinement TLS group | Selection details: all |