+Open data
-Basic information
Entry | Database: PDB / ID: 7bwl | ||||||
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Title | Structure of antibiotic sequester from Pseudomonas aerurinosa | ||||||
Components | UPF0312 protein PA0423 | ||||||
Keywords | ANTIBIOTIC / lipocalin family / antibiotic sequester / antibiotic resistance | ||||||
Function / homology | Uncharacterised protein family UPF0312/YceI / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / periplasmic space / extracellular space / Ubiquinone-8 / UPF0312 protein PA0423 Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Hong, M. | ||||||
Funding support | Korea, Democratic People's Republic Of, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Crystal structure of the Pseudomonas aeruginosa PA0423 protein and its functional implication in antibiotic sequestration. Authors: Lee, C. / Kim, M.I. / Park, J. / Kim, J. / Oh, H. / Cho, Y. / Son, J. / Jeon, B.Y. / Ka, H. / Hong, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bwl.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bwl.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/7bwl ftp://data.pdbj.org/pub/pdb/validation_reports/bw/7bwl | HTTPS FTP |
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-Related structure data
Related structure data | 1wubS 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: 20803.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA0423 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I690 |
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#2: Chemical | ChemComp-UQ8 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: in 0.2 M Sodium chloride, 0.1 M Na/K phosphate pH 6.2, and 40 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 15025 / % possible obs: 99.7 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.026 / Rrim(I) all: 0.089 / Χ2: 1.689 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.053 / Num. unique obs: 846 / CC1/2: 0.998 / Rpim(I) all: 0.018 / Rrim(I) all: 0.056 / Χ2: 1.765 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WUB Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.597 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.231 / Details: U VALUES : WITH TLS ADDED
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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: 94.46 Å2 / Biso mean: 48.194 Å2 / Biso min: 30.12 Å2
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Refinement step | Cycle: final / Resolution: 2.25→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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