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- PDB-6ump: Crystal structure of MavC in complex with substrate mimic in P65 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ump | ||||||
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Title | Crystal structure of MavC in complex with substrate mimic in P65 space group | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Puvar, K. / Iyer, S. / Luo, Z.Q. / Das, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Legionella effector MavC targets the Ube2N~Ub conjugate for noncanonical ubiquitination. Authors: Puvar, K. / Iyer, S. / Fu, J. / Kenny, S. / Negron Teron, K.I. / Luo, Z.Q. / Brzovic, P.S. / Klevit, R.E. / Das, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 98.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6p5bC ![]() 6p5hC ![]() 6ulhC ![]() 6umsC ![]() 1ubqS ![]() 2c2vS ![]() 5tscS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 44194.945 Da / Num. of mol.: 1 / Mutation: C74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 17157.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P61088, ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.64 % / Description: needle/rodlike |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium formate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2019 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→30.75 Å / Num. obs: 17247 / % possible obs: 99.75 % / Redundancy: 10.2 % / Biso Wilson estimate: 66.93 Å2 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.067 / Rrim(I) all: 0.212 / Net I/σ(I): 15.13 |
Reflection shell | Resolution: 2.8→2.85 Å / Mean I/σ(I) obs: 1.17 / Num. unique obs: 957 / CC1/2: 0.514 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5TSC, 1UBQ, 2C2V Resolution: 2.8→30.746 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.87 Å2 / Biso mean: 67.3709 Å2 / Biso min: 27.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→30.746 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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