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Yorodumi- PDB-6w5q: Structure of the globular C-terminal domain of P. aeruginosa LpoP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w5q | ||||||
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Title | Structure of the globular C-terminal domain of P. aeruginosa LpoP | ||||||
Components | Peptidoglycan synthase activator LpoP | ||||||
Keywords | PROTEIN BINDING / Lipoprotein / Activator / Cell Wall | ||||||
Function / homology | : / TPR repeat region circular profile. / Tetratricopeptide-like helical domain superfamily / TRIETHYLENE GLYCOL / TPR_REGION domain-containing protein Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Caveney, N.A. / Robb, C.S. / Simorre, J.P. / Strynadka, N.C.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Structure / Year: 2020 Title: Structure of the Peptidoglycan Synthase Activator LpoP in Pseudomonas aeruginosa. Authors: Caveney, N.A. / Egan, A.J.F. / Ayala, I. / Laguri, C. / Robb, C.S. / Breukink, E. / Vollmer, W. / Strynadka, N.C.J. / Simorre, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w5q.cif.gz | 166.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w5q.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 6w5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w5q_validation.pdf.gz | 504.7 KB | Display | wwPDB validaton report |
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Full document | 6w5q_full_validation.pdf.gz | 514.7 KB | Display | |
Data in XML | 6w5q_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 6w5q_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/6w5q ftp://data.pdbj.org/pub/pdb/validation_reports/w5/6w5q | HTTPS FTP |
-Related structure data
Related structure data | 5xw7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 12133.508 Da / Num. of mol.: 8 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa / Gene: PA4699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HV97 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PGE / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.1 Å3/Da / Density % sol: 41.42 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: (30 mg/mL purified protein in 20 mM HEPES, pH 8.0, 150 mM NaCl) and 1 uL of mother liquor (0.1 M HEPES pH 7.5, 2.5 M ammonium sulfate, 1% PEG 400, 2.5% 1,2-butanediol) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→48.76 Å / Num. obs: 39974 / % possible obs: 98.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 33.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Net I/σ(I): 12.7 / Num. measured all: 129787 / Scaling rejects: 68 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: homology model based on 5XW7 Resolution: 2.2→48.757 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.87 Å2 / Biso mean: 41.759 Å2 / Biso min: 20.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→48.757 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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