+Open data
-Basic information
Entry | Database: PDB / ID: 6lol | ||||||
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Title | The crystal structure of full length IpaH9.8 | ||||||
Components | E3 ubiquitin-protein ligase ipaH9.8 | ||||||
Keywords | TRANSFERASE / E3 / IpaH9.8 | ||||||
Function / homology | Function and homology information modulation of process of another organism / protein K27-linked ubiquitination / host cell cytosol / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell nucleus / extracellular region Similarity search - Function | ||||||
Biological species | Shigella flexneri 2002017 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Ye, Y. / Huang, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Biol / Year: 2020 Title: Substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of bacterial ubiquitin ligase IpaH9.8. Authors: Ye, Y. / Xiong, Y. / Huang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lol.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lol.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lol_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 6lol_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 6lol_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6lol_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/6lol ftp://data.pdbj.org/pub/pdb/validation_reports/lo/6lol | HTTPS FTP |
-Related structure data
Related structure data | 6lojC 5b0tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 59922.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2002017 (bacteria) / Strain: 2002017 / Gene: ipaH9.8, SFxv_5076 / Production host: Escherichia coli (E. coli) References: UniProt: D2AJU0, RING-type E3 ubiquitin transferase |
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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: 4.09 Å3/Da / Density % sol: 73.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 3.0M NaCl, 0.1M Na Citrate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→86.91 Å / Num. obs: 25746 / % possible obs: 99.46 % / Redundancy: 6.6 % / Biso Wilson estimate: 81.01 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.0873 / Net I/σ(I): 15.74 |
Reflection shell | Resolution: 2.75→2.848 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.56 / Num. unique obs: 2524 / CC1/2: 0.862 / CC star: 0.962 / % possible all: 99.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B0T Resolution: 2.75→86.91 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.28 / 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: 211.09 Å2 / Biso mean: 102.7644 Å2 / Biso min: 40.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→86.91 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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