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Yorodumi- PDB-3pjw: Structure of Pseudomonas fluorescence LapD GGDEF-EAL dual domain, I23 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pjw | ||||||
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Title | Structure of Pseudomonas fluorescence LapD GGDEF-EAL dual domain, I23 | ||||||
Components | Cyclic dimeric GMP binding protein | ||||||
Keywords | LYASE / GGDEF-EAL tandem domain / c-di-GMP receptor | ||||||
Function / homology | Function and homology information nucleotide binding / signal transduction / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1006 Å | ||||||
Authors | Sondermann, H. / Navarro, M.V.A.S. | ||||||
Citation | Journal: Plos Biol. / Year: 2011 Title: Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis. Authors: Navarro, M.V. / Newell, P.D. / Krasteva, P.V. / Chatterjee, D. / Madden, D.R. / O'Toole, G.A. / Sondermann, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pjw.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pjw.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 3pjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/3pjw ftp://data.pdbj.org/pub/pdb/validation_reports/pj/3pjw | 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: 47804.934 Da / Num. of mol.: 1 / Fragment: UNP Residues 220-648 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: lapD, Pfl01_0131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KK31 |
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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: 3.24 Å3/Da / Density % sol: 61.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate, 15% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 11371 / Num. obs: 11246 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3.1→3.29 Å / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1006→48.966 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 30.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.39 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1006→48.966 Å
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Refine LS restraints |
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LS refinement shell |
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