+Open data
-Basic information
Entry | Database: PDB / ID: 8wjd | ||||||
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Title | Structure of SptTad2 complexed with cGG | ||||||
Components | SptTad2 | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Chem-C2E Function and homology information | ||||||
Biological species | Sphingobacterium thalpophilum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Xiao, Y. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of SptTad2 complexed with cGG 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 | 8wjd.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wjd.ent.gz | 23.1 KB | Display | PDB format |
PDBx/mmJSON format | 8wjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wjd_validation.pdf.gz | 828.9 KB | Display | wwPDB validaton report |
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Full document | 8wjd_full_validation.pdf.gz | 829 KB | Display | |
Data in XML | 8wjd_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 8wjd_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/8wjd ftp://data.pdbj.org/pub/pdb/validation_reports/wj/8wjd | 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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Unit cell |
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-Components
#1: Protein | Mass: 11598.178 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobacterium thalpophilum (bacteria) Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-C2E / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Magnesium nitrate hexahydrate, Tris pH8.0, PEG2000 |
-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 20, 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: 1.71→48.76 Å / Num. obs: 12316 / % possible obs: 99.2 % / Redundancy: 35.3 % / Rrim(I) all: 0.093 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.71→1.75 Å / Num. unique obs: 881 / Rrim(I) all: 2.406 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→32.5 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.57 / 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: 1.71→32.5 Å
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Refine LS restraints |
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LS refinement shell |
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