+Open data
-Basic information
Entry | Database: PDB / ID: 5ia8 | ||||||
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Title | Structure of a Ubiquitin like protein with an E1 fragment | ||||||
Components | Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier 1 | ||||||
Keywords | CELL CYCLE / Ubiquitin like protein | ||||||
Function / homology | Function and homology information UFM1 activating enzyme activity / ubiquitin-like modifier activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / localization ...UFM1 activating enzyme activity / ubiquitin-like modifier activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / localization / response to endoplasmic reticulum stress / erythrocyte differentiation / brain development / Antigen processing: Ubiquitination & Proteasome degradation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Oweis, W. / Padala, P. / Wiener, R. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence. Authors: Padala, P. / Oweis, W. / Mashahreh, B. / Soudah, N. / Cohen-Kfir, E. / Todd, E.A. / Berndsen, C.E. / Wiener, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ia8.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ia8.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ia8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/5ia8 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/5ia8 | HTTPS FTP |
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-Related structure data
Related structure data | 5ia7C 5iaaS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: -11 - 77 / Label seq-ID: 3 - 91
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-Components
#1: Protein | Mass: 10575.112 Da / Num. of mol.: 2 / Fragment: UNP residues 334-346,UNP residues 1-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UFM1, C13orf20, BM-002 / Production host: Escherichia coli (E. coli) References: UniProt: E7EQ61, UniProt: P61960, UniProt: Q9GZZ9*PLUS #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: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M Potassium phosphate dibasic and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.3 Å / Num. obs: 16255 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.096 |
Reflection shell | Highest resolution: 2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5iaa Resolution: 2→50.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.074 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.956 Å2
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Refinement step | Cycle: 1 / Resolution: 2→50.3 Å
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Refine LS restraints |
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