+Open data
-Basic information
Entry | Database: PDB / ID: 4n88 | ||||||
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Title | Crystal structure of Tse3-Tsi3 complex with calcium ion | ||||||
Components | (Uncharacterized protein) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / lysozyme / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information host cell membrane / lysozyme / lysozyme activity / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Shang, G.J. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2014 Title: Structural insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex from Pseudomonas aeruginosa reveal a calcium-dependent membrane-binding mechanism Authors: Lu, D. / Shang, G. / Zhang, H. / Yu, Q. / Cong, X. / Yuan, J. / He, F. / Zhu, C. / Zhao, Y. / Yin, K. / Chen, Y. / Hu, J. / Zhang, X. / Yuan, Z. / Xu, S. / Hu, W. / Cang, H. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n88.cif.gz | 213.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n88.ent.gz | 169.4 KB | Display | PDB format |
PDBx/mmJSON format | 4n88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/4n88 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/4n88 | HTTPS FTP |
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-Related structure data
Related structure data | 4m5eC 4m5fC 4n7sSC 4n80C C: citing same article (ref.) 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 43618.031 Da / Num. of mol.: 2 / Fragment: UNP residues 2-402 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3484 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYC5 #2: Protein | Mass: 13634.102 Da / Num. of mol.: 2 / Fragment: UNP residues 27-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3485 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYC4 #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.8 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 0.2M Ammonium acetate, 0.01M calcium chloride,0.05M Sodium cacodylate pH 6.5, 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2013 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 34326 / % possible obs: 99.9 % / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N7S Resolution: 2.8→41.384 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 27.42 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.596 Å2 / ksol: 0.281 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→41.384 Å
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Refine LS restraints |
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LS refinement shell |
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