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- PDB-7esp: Structure and mutation analysis of the hexameric P4 from Pseudomo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7esp | ||||||
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Title | Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY | ||||||
![]() | Packaging NTPase | ||||||
![]() | HYDROLASE / Cystoviruses / phiYY P4 / NTPase / VIRAL PROTEIN | ||||||
Function / homology | Packaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / viral genome packaging / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / DI(HYDROXYETHYL)ETHER / D(-)-TARTARIC ACID / Packaging NTPase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, C.Y. / Jin, T.C. | ||||||
![]() | ![]() Title: Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY. Authors: Zhang, C. / Li, Y. / Samad, A. / Zheng, P. / Ji, Z. / Chen, F. / Zhang, H. / Jin, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 400 KB | Display | ![]() |
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PDB format | ![]() | 325.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 77.6 KB | Display | |
Data in CIF | ![]() | 104.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7esoC ![]() 7esqC ![]() 7esvC ![]() 4blpS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37338.531 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: phiYY_sL4 / Production host: ![]() ![]() #2: Chemical | ChemComp-TAR / #3: Chemical | ChemComp-PEG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 200 mM NH4 tartrate, 20% PEG2000 MME, phosphate pH 7.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→40.97 Å / Num. obs: 1250846 / % possible obs: 97.8 % / Redundancy: 10.3 % / CC1/2: 0.998 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.43→2.56 Å / Num. unique obs: 198187 / CC1/2: 0.834 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4blp Resolution: 2.43→40.97 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 24.32 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.52 Å2 / Biso mean: 61.5639 Å2 / Biso min: 34.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.43→40.97 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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