+Open data
-Basic information
Entry | Database: PDB / ID: 6gum | ||||||
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Title | Structure of the A.thaliana E1 UFD domain in complex with E2 | ||||||
Components |
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Keywords | TRANSFERASE / SUMOylation complex | ||||||
Function / homology | Function and homology information SUMO activating enzyme complex / SUMO activating enzyme activity / protein modification by small protein conjugation / SUMO conjugating enzyme activity / embryo development ending in seed dormancy / SUMO binding / response to abscisic acid / plasmodesma / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity ...SUMO activating enzyme complex / SUMO activating enzyme activity / protein modification by small protein conjugation / SUMO conjugating enzyme activity / embryo development ending in seed dormancy / SUMO binding / response to abscisic acid / plasmodesma / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / protein sumoylation / kinase binding / transferase activity / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å | ||||||
Authors | Liu, B. / Lois, L.M. / Reverter, D. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Biochem.J. / Year: 2019 Title: Structural insights into SUMO E1-E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution. Authors: Liu, B. / Lois, L.M. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gum.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gum.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 6gum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gum_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 6gum_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 6gum_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 6gum_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/6gum ftp://data.pdbj.org/pub/pdb/validation_reports/gu/6gum | HTTPS FTP |
-Related structure data
Related structure data | 6gv3C 1a3sS 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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Unit cell |
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-Components
#1: Protein | Mass: 20180.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SCE1, AHUS5, EMB1637, At3g57870, T10K17.80 / Production host: Escherichia coli (E. coli) References: UniProt: Q42551, Transferases; Acyltransferases; Aminoacyltransferases |
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#2: Protein | Mass: 23340.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At2g16970 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178VMI9, UniProt: Q9SJT1*PLUS |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15% PEG6000, 5% Glycerol |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97923 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.792→58.81 Å / Num. obs: 26999 / % possible obs: 97.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.061 / Rrim(I) all: 0.108 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.792→1.798 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A3S Resolution: 1.792→45.08 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.792→45.08 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 12.2417 Å / Origin y: 3.1294 Å / Origin z: 95.0098 Å
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Refinement TLS group | Selection details: all |