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Yorodumi- PDB-4etx: Crystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4etx | ||||||
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Title | Crystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1 | ||||||
Components | PelDPediatric end-stage liver disease | ||||||
Keywords | SIGNALING PROTEIN / c-di-GMP | ||||||
Function / homology | Function and homology information extracellular polysaccharide biosynthetic process / cyclic-di-GMP binding / single-species biofilm formation / membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Li, Z. / Chen, J. / Nair, S.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structures of the PelD Cyclic Diguanylate Effector Involved in Pellicle Formation in Pseudomonas aeruginosa PAO1. Authors: Li, Z. / Chen, J.H. / Hao, Y. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4etx.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4etx.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 4etx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/4etx ftp://data.pdbj.org/pub/pdb/validation_reports/et/4etx | 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: 33712.344 Da / Num. of mol.: 1 / Fragment: UNP residues 155-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3061, pelD / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta(DE3) / References: UniProt: Q9HZE7 |
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#2: 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: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 8 Details: 100 mM Tris, pH 8, 200 mM MgCl2, 10% (v/v) PEG 8000, hanging drop, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Highest resolution: 2 Å / Num. obs: 19307 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.15 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.69 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.015 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.25 Å2 / Biso mean: 42.27 Å2 / Biso min: 8.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -4.2278 Å / Origin y: 1.5679 Å / Origin z: 15.0848 Å
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