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Yorodumi- PDB-7esq: Structure and mutation analysis of the hexameric P4 from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7esq | ||||||
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Title | Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY | ||||||
Components | Packaging NTPase | ||||||
Keywords | 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 / PYROPHOSPHATE / Packaging NTPase Function and homology information | ||||||
Biological species | Pseudomonas phage phiYY (bacteriophage) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Zhang, C.Y. / Jin, T.C. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7esq.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7esq.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 7esq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7esq_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7esq_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7esq_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 7esq_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/7esq ftp://data.pdbj.org/pub/pdb/validation_reports/es/7esq | HTTPS FTP |
-Related structure data
Related structure data | 7esoC 7espC 7esvC 4blpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37338.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phiYY (bacteriophage) Gene: phiYY_sL4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9AK63 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.75 Å3/Da / Density % sol: 55.34 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 26, 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: 1.85→40.13 Å / Num. obs: 687024 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC1/2: 1 / Net I/σ(I): 26.68 |
Reflection shell | Resolution: 1.85→1.96 Å / Num. unique obs: 112408 / CC1/2: 0.718 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4blp Resolution: 1.85→40.13 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.35 / 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: 102.12 Å2 / Biso mean: 45.7793 Å2 / Biso min: 29.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→40.13 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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