+Open data
-Basic information
Entry | Database: PDB / ID: 8wje | ||||||
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Title | Structure of apo-SPO1 Tad2 | ||||||
Components | Gp34.65 | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Protein of unknown function DUF2829 / Protein of unknown function (DUF2829) / metal ion binding / Thoeris anti-defense 2 Function and homology information | ||||||
Biological species | Bacillus phage SPO1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Xiao, Y. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of apo-SPO1 Tad2 Authors: Xiao, Y. / Feng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wje.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wje.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 8wje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wje_validation.pdf.gz | 481.3 KB | Display | wwPDB validaton report |
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Full document | 8wje_full_validation.pdf.gz | 494.5 KB | Display | |
Data in XML | 8wje_validation.xml.gz | 24 KB | Display | |
Data in CIF | 8wje_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/8wje ftp://data.pdbj.org/pub/pdb/validation_reports/wj/8wje | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10787.275 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage SPO1 (virus) / Gene: 34.65 / Production host: Escherichia coli (E. coli) / References: UniProt: B6V311 #2: Water | ChemComp-HOH / | |
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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: 2.96 Å3/Da / Density % sol: 58.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate,Sodium citrate tribasic dihydrate pH5.6, Lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 14, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→35.19 Å / Num. obs: 32017 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.072 / Rrim(I) all: 0.185 / Χ2: 0.87 / Net I/σ(I): 8.9 / Num. measured all: 210831 |
Reflection shell | Resolution: 2.27→2.33 Å / % possible obs: 98.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 2.055 / Num. measured all: 15789 / Num. unique obs: 2339 / CC1/2: 0.445 / Rpim(I) all: 0.849 / Rrim(I) all: 2.227 / Χ2: 0.75 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→33.63 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.74 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→33.63 Å
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Refine LS restraints |
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LS refinement shell |
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