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- PDB-7ycw: Crystal Form 1 of Truncated Antitoxin ParD (2-54,containg RHH dom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ycw | ||||||
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Title | Crystal Form 1 of Truncated Antitoxin ParD (2-54,containg RHH domain) from Pseudoalteromonas rubra | ||||||
![]() | Antitoxin ParD | ||||||
![]() | ANTITOXIN / RHH / Transcription Factor / Toxin antitoxin system | ||||||
Function / homology | Antitoxin ParD superfamily / Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Ribbon-helix-helix / regulation of DNA-templated transcription / Antitoxin ParD![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C.C. / Niu, C.Y. / Niu, L.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the PrpTA toxin-antitoxin system in Pseudoalteromonas rubra. Authors: Wang, C. / Niu, C. / Hidayatullah, K.M. / Xue, L. / Zhu, Z. / Niu, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 38.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.9 KB | Display | ![]() |
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Full document | ![]() | 453.5 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ycsC ![]() 7ycuC ![]() 7ycvC ![]() 7b22S S: Starting model for refinement C: citing same article ( |
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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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7066.906 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Sodium acetate trihydrate,0.1 M Sodium citrate pH 5.5, 5 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30.78 Å / Num. obs: 13454 / % possible obs: 99.71 % / Observed criterion σ(I): 3 / Redundancy: 24.1 % / Biso Wilson estimate: 43.48 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06929 / Rpim(I) all: 0.01471 / Rrim(I) all: 0.07089 / Net I/σ(I): 30.41 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 5.95 / Num. unique obs: 1294 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.1194 / Rrim(I) all: 0.613 / % possible all: 98.92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7B22 Resolution: 2.2→30.78 Å / SU ML: 0.2369 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1627 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30.78 Å
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Refine LS restraints |
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LS refinement shell |
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