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Yorodumi- PDB-4etz: Crystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4etz | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 4etz.cif.gz | 242.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4etz.ent.gz | 197.1 KB | Display | PDB format |
PDBx/mmJSON format | 4etz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/4etz ftp://data.pdbj.org/pub/pdb/validation_reports/et/4etz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33426.098 Da / Num. of mol.: 2 / Fragment: UNP residues 158-454 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 #2: Chemical | #3: 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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 8.5 Details: 100 mM Tris, pH 8.5, 200 mM Li2SO4, and 1.26 M (NH4)2SO4, 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: 2.05 Å / Num. obs: 40304 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.001 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.68 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.433 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.204 / 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: 74.53 Å2 / Biso mean: 53.403 Å2 / Biso min: 12.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / 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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