+Open data
-Basic information
Entry | Database: PDB / ID: 6h78 | ||||||
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Title | E1 enzyme for ubiquitin like protein activation. | ||||||
Components | Ubiquitin-like modifier-activating enzyme 5 | ||||||
Keywords | TRANSFERASE / Ubiquitin like protein activating enzyme | ||||||
Function / homology | Function and homology information UFM1 activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / localization / response to endoplasmic reticulum stress / erythrocyte differentiation ...UFM1 activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / localization / response to endoplasmic reticulum stress / erythrocyte differentiation / Antigen processing: Ubiquitination & Proteasome degradation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / protein homodimerization activity / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Soudah, N. / Padala, P. / Hassouna, F. / Mashahreh, B. / Lebedev, A.A. / Isupov, M.N. / Cohen-Kfir, E. / Wiener, R. | ||||||
Funding support | 1items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation. Authors: Soudah, N. / Padala, P. / Hassouna, F. / Kumar, M. / Mashahreh, B. / Lebedev, A.A. / Isupov, M.N. / Cohen-Kfir, 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 | 6h78.cif.gz | 888.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h78.ent.gz | 735.7 KB | Display | PDB format |
PDBx/mmJSON format | 6h78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/6h78 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/6h78 | HTTPS FTP |
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-Related structure data
Related structure data | 6h77C 3h8vS 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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Unit cell |
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-Components
-Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP
#1: Protein | Mass: 33284.230 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZZ9 |
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-Non-polymers , 6 types, 954 molecules
#2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / | #7: 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: 3.15 Å3/Da / Density % sol: 60.91 % |
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Crystal grow | Temperature: 293.13 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→107.98 Å / Num. obs: 156266 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / CC1/2: 0.979 / Rmerge(I) obs: 0.176 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.447 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7783 / CC1/2: 0.163 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H8V Resolution: 2.7→107.98 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / ESU R: 0.932 / ESU R Free: 0.33
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.184 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→107.98 Å
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Refine LS restraints |
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