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- PDB-7pk5: Phosphodiesterase PdeL (EAL domain of crystals comprising full-le... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pk5 | ||||||
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Title | Phosphodiesterase PdeL (EAL domain of crystals comprising full-length protein) | ||||||
![]() | Cyclic di-GMP phosphodiesterase PdeL | ||||||
![]() | HYDROLASE / c-di-GMP / phosphodiesterase / DNA binding | ||||||
Function / homology | ![]() cyclic-guanylate-specific phosphodiesterase / cyclic-guanylate-specific phosphodiesterase activity / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / protein homodimerization activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Fadel, J. / Schirmer, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Phosphodiesterase PdeL (EAL domain of crystals comprising full-length protein) Authors: Schirmer, T. / Fadel, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.2 KB | Display | ![]() |
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PDB format | ![]() | 165.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.2 KB | Display | ![]() |
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Full document | ![]() | 477 KB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 45.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lykS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41669.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: pdeL, yahA, b0315, JW0307 / Production host: ![]() ![]() References: UniProt: P21514, cyclic-guanylate-specific phosphodiesterase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.3 M Sodium acetate trihydrate 0.1 M Tris 7.5 8 % w/v PEG 20,000 8 % v/v PEG 500 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 15, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 4.4→48.41 Å / Num. obs: 16934 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.053 / Rrim(I) all: 0.142 / Net I/σ(I): 7.8 / Num. measured all: 120886 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4lyk Resolution: 4.4→25 Å / Cor.coef. Fo:Fc: 0.829 / Cor.coef. Fo:Fc free: 0.703 / SU B: 0.023 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.184 / ESU R Free: 1.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 186.58 Å2 / Biso mean: 112.145 Å2 / Biso min: 73.53 Å2
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Refinement step | Cycle: final / Resolution: 4.4→25 Å
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LS refinement shell | Resolution: 4.4→4.511 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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