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Yorodumi- PDB-4iob: Crystal structure of the GGDEF domain of PA1120 (YfiN or TpbB) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iob | ||||||
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Title | Crystal structure of the GGDEF domain of PA1120 (YfiN or TpbB) from Pseudomonas aeruginosa at 2.7 Ang. | ||||||
Components | Diguanylate cyclase TpbB | ||||||
Keywords | LYASE / TpbB / YfiN / ggdef / DGC / PF00990 / Diguanylate cyclase / GTP / c-di-GMP / cGpGp / cytosolic portion of a membrane protein | ||||||
Function / homology | Function and homology information diguanylate cyclase / diguanylate cyclase activity / metabolic process / GTP binding / signal transduction / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||
Authors | Giardina, G. / Cutruzzola, F. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Investigating the Allosteric Regulation of YfiN from Pseudomonas aeruginosa: Clues from the Structure of the Catalytic Domain. Authors: Giardina, G. / Paiardini, A. / Fernicola, S. / Franceschini, S. / Rinaldo, S. / Stelitano, V. / Cutruzzola, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iob.cif.gz | 44 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iob.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 4iob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iob_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 4iob_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 4iob_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 4iob_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/4iob ftp://data.pdbj.org/pub/pdb/validation_reports/io/4iob | HTTPS FTP |
-Related structure data
Related structure data | 2wb4S S: Starting model for refinement |
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Similar 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: 17540.955 Da / Num. of mol.: 1 Fragment: Diguanylate cyclase (GGDEF) domain, UNP residues 254-414 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1120, tpbB / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I4L5, diguanylate cyclase |
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#2: Chemical | ChemComp-TBU / |
#3: Chemical | ChemComp-GOL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 300nl+300nl of 3.7 mg/ml protein solution (100 mM NaCl, 10 mM Tris pH=8.0, 2% glycerol) and 0.1 M Sodium Citrate dehydrate pH 5.6, 35% v/v tert-butanol., VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 18, 2012 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→40 Å / Num. all: 4359 / Num. obs: 4343 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 13.7 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.083 / Net I/σ(I): 31.11 |
Reflection shell | Resolution: 2.78→2.94 Å / Redundancy: 9.77 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 3.3 / Num. unique all: 666 / Rsym value: 0.685 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WB4 Resolution: 2.78→40 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.888 / SU B: 16.717 / SU ML: 0.335 / Isotropic thermal model: Isotropic / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.086 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.78→2.849 Å / Total num. of bins used: 20
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