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- PDB-8hm1: crystal structure of human ubiquitin-like protein from Bacteroide... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hm1 | ||||||
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Title | crystal structure of human ubiquitin-like protein from Bacteroides fragilis | ||||||
![]() | Putative ubiquitin | ||||||
![]() | CELL CYCLE / ubiquitin-like protein | ||||||
Function / homology | : / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Ubiquitin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tong, M. / Chen, Z. / Gao, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome. Authors: Jiang, K. / Li, W. / Tong, M. / Xu, J. / Chen, Z. / Yang, Y. / Zang, Y. / Jiao, X. / Liu, C. / Lim, B. / Jiang, X. / Wang, J. / Wu, D. / Wang, M. / Liu, S.J. / Shao, F. / Gao, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.1 KB | Display | ![]() |
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PDB format | ![]() | 35.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 448.7 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hm2C ![]() 8hm3C ![]() 8hm4C ![]() 1ubqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 8878.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium citrate pH 3.0, 3.4 M cesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→32.86 Å / Num. obs: 36628 / % possible obs: 98.07 % / Redundancy: 20 % / Biso Wilson estimate: 16.43 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.29→1.336 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3124 / CC1/2: 0.557 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UBQ Resolution: 1.29→32.86 Å / SU ML: 0.1928 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8666 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 22.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→32.86 Å
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Refine LS restraints |
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LS refinement shell |
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