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- PDB-7ycv: The Dimeric Format of Truncated PrpA (2-54)and RHH Domain of PrpA -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ycv | ||||||
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Title | The Dimeric Format of Truncated PrpA (2-54)and RHH Domain of PrpA | ||||||
![]() | Antitoxin ParD | ||||||
![]() | ANTITOXIN / Toxin antitoxin system / RHH Transcription factor / ParD_antitoxin / Pseudoalteromonas rubra / ANTIMICROBIAL PROTEIN | ||||||
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 | ![]() | 35.6 KB | Display | ![]() |
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PDB format | ![]() | 22.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ycsC ![]() 7ycuC ![]() 7ycwC ![]() 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.: 2 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: 2.17 Å3/Da / Density % sol: 43.32 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30 % v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→30.34 Å / Num. obs: 3976 / % possible obs: 99.25 % / Redundancy: 13.7 % / Biso Wilson estimate: 62.7 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1038 / Rpim(I) all: 0.02865 / Rrim(I) all: 0.108 / Net I/σ(I): 16.46 |
Reflection shell | Resolution: 2.612→2.706 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.8511 / Mean I/σ(I) obs: 2.99 / Num. unique obs: 373 / CC1/2: 0.907 / CC star: 0.975 / Rpim(I) all: 0.2309 / Rrim(I) all: 0.8837 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7B22 Resolution: 2.61→30.34 Å / SU ML: 0.2446 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9639 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: 62.88 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→30.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.61→2.706 Å
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