+Open data
-Basic information
Entry | Database: PDB / ID: 7xed | ||||||
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Title | Crystal Structure of OsCIE1-Ubox and OsUBC8 complex | ||||||
Components |
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Keywords | TRANSFERASE / complex / ubiquitination / Ubox / ligase / PLANT PROTEIN | ||||||
Function / homology | Function and homology information RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / transferase activity / protein ubiquitination / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhang, Y. / Yu, C.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2024 Title: Release of a ubiquitin brake activates OsCERK1-triggered immunity in rice. Authors: Wang, G. / Chen, X. / Yu, C. / Shi, X. / Lan, W. / Gao, C. / Yang, J. / Dai, H. / Zhang, X. / Zhang, H. / Zhao, B. / Xie, Q. / Yu, N. / He, Z. / Zhang, Y. / Wang, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xed.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xed.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xed_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 7xed_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 7xed_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 7xed_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/7xed ftp://data.pdbj.org/pub/pdb/validation_reports/xe/7xed | HTTPS FTP |
-Related structure data
Related structure data | 8hpbC 8hqbC 2oxqS 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: 16540.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: OsJ_21490 / Production host: Escherichia coli (E. coli) / References: UniProt: A3BC59 #2: Protein | Mass: 8952.272 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: PUB12, Os06g0102700, LOC_Os06g01304, OSJNBa0075G19.19-1 Production host: Escherichia coli (E. coli) References: UniProt: Q5VRH9, RING-type E3 ubiquitin transferase #3: 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: 2.71 Å3/Da / Density % sol: 54.59 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 0.3M Calcium acetate, 20% PEG 3350, 0.1M MES |
-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 EIGER2 S 9M / Detector: PIXEL / Date: Nov 21, 2021 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→66.28 Å / Num. obs: 19672 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 75.07 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.5→2.57 Å / Num. unique obs: 1418 / CC1/2: 0.341 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OXQ Resolution: 2.5→43.64 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 29.96 / 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: 137.35 Å2 / Biso mean: 81.4838 Å2 / Biso min: 46.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→43.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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