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Yorodumi- PDB-8u0i: Crystal structure of PA0012 complexed with cyclic-di-GMP from Pse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u0i | ||||||
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Title | Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa | ||||||
Components | PilZ domain-containing protein | ||||||
Keywords | SIGNALING PROTEIN / Complex | ||||||
Function / homology | PilZ domain / PilZ domain / cyclic-di-GMP binding / Chem-C2E / PilZ domain-containing protein Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.541 Å | ||||||
Authors | Hammons, N.A. / Schnicker, N.J. / Fuentes, E.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa Authors: Hammons, N.A. / Schnicker, N.J. / Fuentes, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u0i.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u0i.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 8u0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u0i_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8u0i_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8u0i_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 8u0i_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/8u0i ftp://data.pdbj.org/pub/pdb/validation_reports/u0/8u0i | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9969.399 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: PA0012 / Plasmid: pET21a Details (production host): Modified with an N-terminal cleavable hexa-His tag Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): K-12 / References: UniProt: Q9I7B4 | ||||||
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#2: Chemical | #3: Chemical | #4: 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: 2.88 Å3/Da / Density % sol: 57.38 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 5.3 mg/mL PA0012 and 2.5 mM cyclic-di-GMP. 0.2 M NH4SO4, 15% (w/v) PEG4000, 0.1 M Tri-NaCit pH=5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0004 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→43.99 Å / Num. obs: 17945 / % possible obs: 100 % / Redundancy: 39.2 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.013 / Rrim(I) all: 0.083 / Χ2: 0.27 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 32.9 % / Rmerge(I) obs: 1.064 / Num. unique obs: 865 / CC1/2: 0.971 / Rpim(I) all: 0.187 / Rrim(I) all: 1.08 / Χ2: 0.01 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.541→43.988 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.155 / SU B: 1.612 / SU ML: 0.055 / Average fsc free: 0.9656 / Average fsc work: 0.9708 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.074 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.158 Å2
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Refinement step | Cycle: LAST / Resolution: 1.541→43.988 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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