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Yorodumi- PDB-6zm3: The structure of an E2 ubiquitin-conjugating complex (UBC2-UEV1) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zm3 | |||||||||||||||
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Title | The structure of an E2 ubiquitin-conjugating complex (UBC2-UEV1) essential for Leishmania amastigote differentiation | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Leishmaniasis / Differentiation / Ubiquitin / Conjugation / UBC2-UEV1 complex | |||||||||||||||
Function / homology | Function and homology information ubiquitin-protein ligase / ligase activity / transferase activity / ATP binding Similarity search - Function | |||||||||||||||
Biological species | Leishmania mexicana (eukaryote) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||||||||
Authors | Burge, R.J. / Dodson, E.J. / Wilkinson, A.J. / Mottram, J.C. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: Plos Pathog. / Year: 2020 Title: Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex. Authors: Burge, R.J. / Damianou, A. / Wilkinson, A.J. / Rodenko, B. / Mottram, J.C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zm3.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zm3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zm3_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 6zm3_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 6zm3_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 6zm3_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/6zm3 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zm3 | HTTPS FTP |
-Related structure data
Related structure data | 1j7dS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 17298.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (strain MHOM/GT/2001/U1103) (eukaryote) Strain: MHOM/GT/2001/U1103 / Gene: LMXM_04_0680 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: E9AK51, ubiquitin-protein ligase #2: Protein | Mass: 16279.417 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (strain MHOM/GT/2001/U1103) (eukaryote) Strain: MHOM/GT/2001/U1103 / Gene: LMXM_13_1580 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: E9API2, ubiquitin-protein ligase #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.16 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: UBC2 and UEV1 were mixed in a 1:1 molar ratio to a final concentration of 6.6 mg mL-1 and incubated on ice for 30 min. Crystals were grown using a sitting drop method with a 1:1 ratio of ...Details: UBC2 and UEV1 were mixed in a 1:1 molar ratio to a final concentration of 6.6 mg mL-1 and incubated on ice for 30 min. Crystals were grown using a sitting drop method with a 1:1 ratio of protein to reservoir solution (0.1 M Bis-Tris propane, pH 7.5, 0.2 M sodium formate and 20% PEG) in the drop. Crystals took 2 days to appear. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å | ||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2019 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.65→47.25 Å / Num. obs: 67149 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.075 / Rrim(I) all: 0.12 / Net I/σ(I): 6.7 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 4.2 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 1J7D Resolution: 1.7→46.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.71 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.131
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.043 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→46.25 Å
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Refine LS restraints |
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LS refinement shell |
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