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Yorodumi- PDB-6jfw: Crystal structure of PA0833 periplasmic domain from Pseudomonas a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jfw | ||||||
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Title | Crystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket | ||||||
Components | PA0833-PD protein | ||||||
Keywords | MEMBRANE PROTEIN / Pseudomonas aeruginosa / OmpA C-like protein / PA0833 / PGN-binding basis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å | ||||||
Authors | Lin, X. / Ye, F. / Lin, S. / Yang, F.L. / Chen, Z.M. / Cao, Y. / Chen, Z.J. / Gu, J. / Lu, G.W. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Crystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket. Authors: Lin, X. / Ye, F. / Lin, S. / Yang, F. / Chen, Z. / Cao, Y. / Chen, Z. / Gu, J. / Lu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jfw.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jfw.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jfw_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 6jfw_full_validation.pdf.gz | 457.4 KB | Display | |
Data in XML | 6jfw_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 6jfw_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/6jfw ftp://data.pdbj.org/pub/pdb/validation_reports/jf/6jfw | HTTPS FTP |
-Related structure data
Related structure data | 2k1sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 17499.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0833 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9I5A7 #2: 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: 1.93 Å3/Da / Density % sol: 36.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium sulfate, 0.1M Sodium acetate (pH 4.6), 25% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97923 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 34416 / % possible obs: 97.8 % / Redundancy: 3.9 % / Rsym value: 0.105 / Net I/σ(I): 13.043 |
Reflection shell | Resolution: 2→2.07 Å / Rsym value: 0.414 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2K1S Resolution: 2.002→28.436 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 21.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.002→28.436 Å
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Refine LS restraints |
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LS refinement shell |
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